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Archives of Biochemistry and Biophysics 602 (2016) 61e68

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Assessment of microcrystal quality by transmission electron

microscopy for efcient serial femtosecond crystallography*
Christopher O. Barnes a, b, 1, Elena G. Kovaleva c, 1, Xiaofeng Fu a, Hilary P. Stevenson a,
Aaron S. Brewster d, Daniel P. DePonte e, Elizabeth L. Baxter c, Aina E. Cohen c, **,
Guillermo Calero a, *
Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
Stanford Synchrotron Radiation Lightsource, Menlo Park, CA 94025, USA
Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
Linac Coherent Light Source, Menlo Park, CA 94025, USA

a r t i c l e i n f o a b s t r a c t

Article history: Serial femtosecond crystallography (SFX) employing high-intensity X-ray free-electron laser (XFEL)
Received 10 December 2015 sources has enabled structural studies on microcrystalline protein samples at non-cryogenic tempera-
Received in revised form tures. However, the identication and optimization of conditions that produce well diffracting micro-
4 February 2016
crystals remains an experimental challenge. Here, we report parallel SFX and transmission electron
Accepted 6 February 2016
Available online 2 March 2016
microscopy (TEM) experiments using fragmented microcrystals of wild type (WT) homoprotocatechuate
2,3-dioxygenase (HPCD) and an active site variant (H200Q). Despite identical crystallization conditions
and morphology, as well as similar crystal size and density, the indexing efciency of the diffraction data
Transmission electron microscopy
collected using the H200Q variant sample was over 7-fold higher compared to the diffraction results
Serial femtosecond crystallography obtained using the WT sample. TEM analysis revealed an abundance of protein aggregates, crystal
X-ray free electron laser conglomerates and a smaller population of highly ordered lattices in the WT sample as compared to the
Liquid-jet injector H200Q variant sample. While not reported herein, the 1.75 resolution structure of the H200Q variant
was determined from ~16 min of beam time, demonstrating the utility of TEM analysis in evaluating
sample monodispersity and lattice quality, parameters critical to the efciency of SFX experiments.
2016 Elsevier Inc. All rights reserved.

1. Introduction crystals to the XFEL pulses. Unlike more conventional goniometer-

based crystallography experiments, where one or a few crystals at
The X-ray Free Electron Laser (XFEL) has advanced the eld of X- cryogenic temperatures are used to obtain a complete dataset,
ray crystallography by enabling structure determination using ra- liquid injector serial femtosecond crystallography (SFX) experi-
diation sensitive sub-micrometer sized crystals [2,14,26,31]. X-ray ments are contingent upon the collection of several thousand
damage is overcome through the use of ultrashort X-ray pulses that diffraction patterns often using millions of crystals delivered in
produce a diffraction pattern before radiation induced structural random orientations [4,18,28].
rearrangements occur within the crystal. These experiments are Such injector systems have been successful for high resolution
often conducted in a serial mode using liquid injectors to deliver structure determination at near physiological temperatures
[4,6,10,16,23,28,39]. For these experiments, crystal slurries are
focused into a continuous liquid jet that delivers single crystals of a
few microns to submicron dimensions to the XFEL pulses. Recently,
This article is part of a Special Issue entitled Protein Crystallography, edited by development of viscous media injectors have lessened sample
Ana Camara-Artigas and Jose Antonio Gavira.
consumption, a major drawback of liquid injector-based SFX ex-
* Corresponding author.
** Corresponding author.
periments, by signicantly reducing the sample ow to better
E-mail addresses: (A.E. Cohen), match the XFEL repetition rate (for example, 120 Hz at the Linac
(G. Calero). Coherent Light Source (LCLS) at the Stanford Linear Accelerator
These authors contributed equally to this work.
0003-9861/ 2016 Elsevier Inc. All rights reserved.
62 C.O. Barnes et al. / Archives of Biochemistry and Biophysics 602 (2016) 61e68

(SLAC) [3,7,9,37,39]. While improvements in liquid injectors and the prior to loading into the sample reservoir for diffraction studies.
analysis of sparse datasets are active and dynamic research areas
involving many groups [10,13,15,27,39], less focus has been geared 2.2. SFX data collection, processing and renement
towards understanding the intrinsic characteristics of microcrys-
talline slurries and their amenability to the injection process. Diffraction data were collected at the CXI end station of LCLS
Properties that could affect injector performance and/or using 8.8 keV X-ray pulses with 40 fs duration and 1 mm beam focus
diffraction quality include crystal concentration, size distribution, at the X-ray interaction point. Sample delivery using gas dynamic
quality and uniformity of the crystal lattices, or the presence of virtual nozzle (GDVN) was carried out at a ow rate of 20 ml/s at
protein and/or crystal aggregates. Various methods have been used 16  C. Diffraction images were collected at 120 Hz using a CSPAD
to identify microcrystals with homogenous physical properties. detector and processed using ccbtx.xfel software package ([13,40]).
Such methods include dynamic light scattering [33], second-order The WT enzyme sample resulted in 814 indexable images during
nonlinear imaging of chiral crystals [24], as well as microuidic 6.7 min of data collection. A total of 15.6 min of data collection
technologies [1,22] and transmission electron microscopy (TEM) using the H200Q variant sample resulted in a dataset based on
[11,28,36]. In the latter case, we previously showed that not only is 14026 merged images. During indexing, secondary lattices indica-
TEM capable of identifying conditions amenable to microcrystal tive of multiple crystals were identied by rst indexing, then
formation, but also is capable of characterizing the intrinsic prop- removing primary lattices and then attempting to index the
erties of the microcrystals (I.E. size, lattice quality, aggregation, etc.) remaining bright reections [13,29].
[35]. In this report, we provide evidence that demonstrates the
utility of TEM in the characterization of microcrystalline slurries to
2.3. Quantication of microcrystal slurries
maximize the success of SFX studies, through the comparative
analysis of homoprotecatechuate 2,3-dioxygenase (HPCD) samples
To quantify the microcrystals, samples were diluted in mother
with signicantly different indexing efciencies.
liquor 300 e fold and a 10 mL aliquot was applied to a bright-line
hemocytometer (Hausser Scientic). Using a Jan Scientic Jansi
2. Experimental procedure
UVEX microscope with nominal 5-, 15-, and 40 magnications the
sample chamber grids were visualized using brighteld and UV
2.1. Enzyme purication, crystallization and sample preparation
uorescence with exposures of 0.1 and 5 s, respectively. Images
were evaluated using the Jan Scientic CrystalDetect software and
Recombinant homoprotocatechuate 2,3-dioxygenase from
nominal 15 magnication images were recorded (Innity 2e3C
B. fuscum (E.C. was expressed in Escherichia coli and pu-
Camera, Lumenera Scientic). Manual quantication was achieved
ried using procedures described previously [12,25]. The enzyme
using the Vi-CELL XR 2.03 software program (Beckman Coulter). A
preparations used in this study included a wild type (WT) enzyme
crystal was dened as having a minimum dimension of 6 pixels
and an active site variant with His200 substituted for Gln (H200Q).
(~2.5 mm), with intensity values 3 standard deviations above the
Previously published crystallization conditions and procedures
background threshold.
that produce diffraction quality macro-crystals of 2,3-HPCD en-
zymes [19e21] were modied for injector-based experiments to
2.4. Transmission electron microscopy
scale up production of micro-crystal slurries using an over-
nucleation approach. Protein solutions (7e10 mg/ml) were gently
Microcrystal samples were analyzed by transmission electron
mixed in a 1:1 ratio with crystallization solution consisting of
microscopy as previously described [34]. Briey, 10 mL of sample
12e14% PEG6000, 0.1 M calcium chloride, and 0.1 M MES pH 5.8,
was applied to glow charged 400 square mesh copper grids with a
ensuring that no precipitate forms at these concentrations of
continuous carbon lm (Electron Microscopy Sciences). Following
components. After a few minutes of equilibration, a 20 mL aliquot of
sample incubation on the grid for 30 s, excess liquid was removed
the 1:1 stock mixture (protein and crystallization solution) was
and the grid stained with 2% (w/v) uranyl acetate. Protein crystal-
seeded with a few roughly crushed macro-crystals in an eppendorf
linity of each sample was determined by screening for the presence
tube, and growth of many needle-like crystals was observed after a
of lattices. Lattice quality was evaluated by performing a fast
few hours of incubation at 20  C. Every 2e4 h 50e200 mL of a fresh
mixture of protein and crystallization solution was added into the
crystallization tubes to maintain maximal growth of needle-like Table 1
crystals, followed by a nal 12 h period of growth to achieve Comparison of physical properties and processing characteristics for the HPCD
saturation in a total of 2e3 ml volume. The WT enzyme preparation samples used for SFX data collection.
produced slightly larger population of initial crystals (thin rods), (H200Q HPCD) (WT HPCD)
whereas the H200Q variant preparation produced slurries with a 8
Density (crystals/ml) 1.2  10 (0.1) 1.53  108 (0.07)
needle-like crystals. Size distributionb
A mixture of glass beads (0.1 and 0.5 mm) was used to crush the a ~ b (mm) 2.5 (0.5) 2.6 (0.6)
crystals to achieve a smaller and more uniform sample size for c (mm) 11.7 (5.6) 10.4 (4.1)
injector-based studies. The WT sample, consisting of thin rods, was Number of Bragg Spotsc 4th order 3rd order
Indexing efciency (%)d 12.2 1.7
vortexed with the glass beads mixture several times at medium to 2nd lattice hits (%)e 16.1 8.4
high speed for 60 s, followed by a 10-min rest period. Slurries of a
Values for crystal density quantication using nominal 15 magnication
needle-like crystals of the H200Q variant were concentrated by
(n 12) as described in Experimental Procedure.
centrifugation at 2000 rpm for 5e10 min prior to the addition of the b
Size distribution for fragmented microcrystal samples was determined manu-
glass beads mixture and additional centrifugation for 2 min. The ally from UV imaging data at nominal 15 magnication (n 15). Mean values for
efciency of crystal crushing using either the vortexing or micro- short (a, b) and long (c) dimensions for rod-like morphology.
centrifugation methods were monitored qualitatively by light mi- Bragg Spot order calculated from FFT transforms of observable lattices (median
derived from n 8).
croscopy, and by visually observing the light scattering of sample d
The percentage of collected images that contained indexed patterns (single hits
medium using a ashlight. Crushed samples were passed thru a and 2nd lattices).
20 mm lter to remove particulates and larger crystalline material e
Percentage of double hits in the total number of indexed patterns.
C.O. Barnes et al. / Archives of Biochemistry and Biophysics 602 (2016) 61e68 63

Fourier transform of the lattice to obtain the reciprocal lattice re- Due to rod/needle-like morphology of HPCD crystals and much
ections or Bragg spots. Bragg spot order of three or above was faster crystal growth in one dimension, fragmentation was required
considered to be of high quality. A single-tile specimen holder was to reduce the length of microcrystals and improve uniformity for
used to deliver samples to a FEI Tecnai T12 electron microscope. The injector-based studies. In addition to vortexing, a commonly used
microscope was operated at 120 kV and images were captured with fragmentation method, sonication, and centrifugation fragmenta-
a 2 k  2 k Gatan UltraScan 1000 CCD camera. tion methods were tested (see section 2). However, because of the
limited amount of beam time allocated for this project, diffraction
experiments for only two bulk fragmentation methods (centrifu-
3. Results
gation or vortexing, for H200Q and WT samples respectively), were
carried out on the CXI instrument (LCLS) using the gas dynamic
3.1. Preparation and SFX data collection of HPCD microcrystalline
virtual nozzle (GDVN) injector [8].
Diffraction data for both samples were collected using the same
experimental settings, as described in the section 2. All still
In this study, microcrystalline suspensions were prepared using
diffraction images acquired during beam time were used for
two HPCD stocks, a WT enzyme and an H200Q variant. The single
indexing and integration with ccbtx.xfel (Table 1). Therefore, to
isosteric substitution in the active site (H200Q) has no effect on the
enable comparison between samples (Fig. 1A and B), the overall
crystal morphology (rod-like), spacegroup, unit cell dimensions or
indexing efciency is dened here as a percentage of the total
diffraction quality as established previously in structural
images, collected at the repetition rate of 120 Hz, which could be
synchrotron-based studies using macrocrystals at cryo-
indexed successfully.
temperatures [21]. Therefore, these enzyme stocks were used to
During 6.7 min of data collection using the WT enzyme sample
account for prep-to-prep variability for optimization of the batch
(which showed a high tendency of nozzle clogging), a total of 814
crystallization procedures.

Fig. 1. Representative observed indexing rates and crystal density quantication for both H200Q and WT HPCD slurries. A plot of the number of indexable patterns observed during
a representative 6 min of data collection using the GDVN injector with the H200Q HPCD microcrystal sample (A) and with the WT HPCD microcrystal sample (B) illustrates the
reduced hit rate observed for the WT sample. The number of indexable hits/second from cctbx.xfel processing are plotted, where the blue trace indicates total number of indexable
images per second and the red trace is the averaged indexing rate every 11 s. Representative hemocytometer quadrants, reconstructed from 4 separate images using a 15 objective
on a JanScientic Jansi UVEX microscope, illustrate fairly similar crystal densities for H200Q (C) and WT (D) slurries. Crystal quantication was achieved for both slurries using
manual counting with ImageJ software (see section 2, scale bars e C,D: 50 mm) (n 12).
64 C.O. Barnes et al. / Archives of Biochemistry and Biophysics 602 (2016) 61e68

diffraction patterns were indexed, corresponding to 1.7% of the total (Table 1), suggesting that crystal density between slurries was not a
images collected (Table 1). The observed indexing efciency of 1.7% contributing factor to the ~7-fold difference in the indexing rate
for the WT enzyme sample compares well with the typical values between them. The occurrence of a second lattice was found in
from previously published SFX studies, where 0.5e4% of the still 16.1% and 8.4% of indexed images for the H200Q and the WT
diffraction images acquired at the same repetition rate (120 Hz) samples, respectively (Table 1). This data suggests that lower crystal
were successfully indexed and merged [4,6,13,32,38]. In contrast, densities may be practical for liquid injector-based experiments.
12.2% of the total images acquired using the H200Q enzyme sample Next, we examined the crystal size distribution using brighteld
during 15.6 min of beam time were successfully indexed (Table 1). and UV microscopy for the WT and the H200Q variant samples
(Table 1). In an effort to reduce clogging of the GDVN injector
3.2. Characterizing microcrystalline density and size distribution nozzle, samples are typically ltered to limit the maximum crystal
size. If the crystal size distribution of the two samples was signif-
We next examined whether differences in the crystal density icantly different, the different indexing rates observed during data
and size of the microcrystalline slurries could explain the 7.3-fold collection could potentially be attributed to increased clogging of
difference in indexing efciency of H200Q vs WT, as these are the GDVN nozzle, which focuses the crystal slurry to a stream of
important considerations for sample delivery and sample con- about 5 mm in diameter. However, our analysis revealed no size
sumption in liquid injector-based experiments. Previously, crystal difference between the WT and the H200Q variant samples
densities of ~109 crystals/mL have been proposed as the benchmark (Table 1). Many of the crystals from both samples were long needles
to attain high hit rates while reducing the occurrence of double hits with a signicant fraction retaining a length of 10e20 mm following
during GDVN experiments [4,17,31], although sample densities of the fragmentation and ltration procedures.
1010 to 1011 crystals/mL are frequently used as well [13,38].
Therefore, in order to quantify accurately the number of crystals for 3.3. Analysis of crystal lattice quality and monodispersity with TEM
both H200Q and the WT slurries, we applied crystal slurries to a
hemocytometer and determined the number of crystals/ml from The homogeneity and intrinsic order of microcrystals are critical
images obtained during UV-microscopy (Fig. 1C and D). Both parameters for SFX studies that also cannot be assessed effectively
samples showed similar crystal densities of ~108 crystals/ml by bright-eld microscopy. Similarities between crystal

Fig. 2. Negative-stain TEM images of HPCD microcrystals. A,B. Representative TEM sampling of H200Q crystals, illustrates sample monodispersity (A), with high quality crystal
lattices (B) as determined from its FFT prole (inset). On average, 4th order Bragg spots were recorded for H200Q crystals. C,D. Representative TEM sampling of WT crystals, il-
lustrates sample aggregation or crystal conglomerates (C), typically not seen with brighteld or UV microscopy. Lattice quality was of high quality (D), with an average of 3rd order
Bragg spots observed for WT samples. (Scale bars e A,C: 0.5 mm; B,D: 50 nm).
C.O. Barnes et al. / Archives of Biochemistry and Biophysics 602 (2016) 61e68 65

Fig. 3. Negative-stain TEM analysis of bulk fragmentation methods for rod-like 2,3 e HPCD microcrystals. A,B. TEM images of H200Q (A) or WT (B) crystals after fractionation with
centrifugation. C,D. TEM images of H200Q (C) or WT (D) crystals after fractionation with vortexing. E,F. TEM images of H200Q (E) or WT (F) crystals after fractionation with
sonication. Lattice quality was evaluated when single crystals were observed and median values of 3rd order Bragg spots (not shown) for all samples across the varying frag-
mentation protocols. (Scale bars e A-F: 1 mm).
66 C.O. Barnes et al. / Archives of Biochemistry and Biophysics 602 (2016) 61e68

Fig. 4. Negative-stain TEM analysis of bulk fragmentation methods for needle-like 2,3 e HPCD microcrystals. A,B. TEM images of H200Q (A) or WT (B) crystals after fractionation
with centrifugation. C,D. TEM images of H200Q (C) or WT (D) crystals after fractionation with vortexing. E,F. TEM images of H200Q (E) or WT (F) crystals after fractionation with
sonication. Lattice quality was evaluated when single crystals were observed and median values of 3rd order Bragg spots (not shown) for all samples across the varying frag-
mentation protocols. (Scale bars e A-F: 1 mm).
C.O. Barnes et al. / Archives of Biochemistry and Biophysics 602 (2016) 61e68 67

morphology, size, and density raise the possibility that observed accessible, it would not provide details beyond the crystallinity of
differences in the indexing efciency may be attributed to the the sample. The usefulness in TEM compared to other sample
quality of the crystal lattice in the two samples. Negative-stain TEM preparation tools (I.E. dynamic light scattering, SONICC, UV-
analysis, conducted on the two microcrystalline samples of HPCD, uorescence, XPD, etc.) is that it not only is capable of identifying
revealed both major differences in the lattice quality and homo- crystalline material, but also provides the experimenter with
geneity (Fig. 2). In addition to higher order Bragg spots (>4th order) additional information about further optimizing or discarding
observed in H200Q crystals, the EM landscape indicated a highly crystals grown under certain conditions [35].
monodispersed sample (Fig. 2A and B). In contrast, WT micro- In addition to microcrystal quality, our data also raises the
crystals showed a high degree of sample aggregation, protein possibility that crystal density may play a greater role in data
conglomerates, and a limited number of crystal lattices with >3rd collection efciency than previously thought. Assessment of our
order Bragg spots (Fig. 2C and D). Moreover, delivery of the WT data and previously published results illustrate negative correlation
sample was prone to nozzle clogging, which would be consistent between increasing overall indexing efciency with decreasing
with the high degree of protein aggregation observed by TEM and crystal densities [4e6,13,28,32,38]. Furthermore, when considering
the low indexing rate for this sample (Fig. 1B). the monodispersed H200Q sample (as visualized by TEM) which
Since bulk fragmentation of the WT and H200Q microcrystals had lower crystal densities than those routinely used for GDVN
differed, we performed TEM experiments on the fragmentation based experiments, we still observed ~20% double lattice hits for
protocols to determine its effects on sample monodispersity, lattice indexed images. This raises the possibility that lower crystal den-
quality and crystal aggregation. While we observed no major sities may be advantageous and practical for liquid-jet experiments.
differences in the lattice quality among HPCD samples prepared by However, since TEM experiments to analyze monodispersity and
different fragmentation methods, we did observe minor differences overall quality of crystal lattices were not performed for previously
in the amount of crystal aggregation. TEM analysis revealed fewer published samples, we cannot rule out that these factors played a
aggregates for crystals fragmented via centrifugation or vortexing role in their overall indexing hit rates. Yet taken together, these data
(with a glass bead cocktail) when compared to crystals prepared by suggest that monodisperse samples analyzed by TEM with crystal
sonication, irrespective of the characteristics of the starting material densities of 108 crystals/mL may improve efciency and lessen
prior to fragmentation (Figs. 3 and 4). Given that cryo-cooled sample consumption, which is applicable to challenging protein
macrocrystals generated for fragmentation of both H200Q and WT targets (I.E. membrane proteins, multi-protein complexes, etc.).
show no difference in diffraction or crystal quality [21], the observed
variance in the indexing rates between the two otherwise similar Author contributions
samples could stem from the differences in monodispersity and
degree of protein or crystal aggregation generated during protein E.G.K conducted crystallization, sample preparation, and X-ray
sample preparation or crystallization experiments. The extent and data collection. A.S.B. and E.L.B performed processing of diffraction
inuence of these factors are speculative and will require additional image data. D.P.D. provided technical assistance with sample de-
testing to demonstrate a clear signicant correlation. livery during XFEL data collection. C.O.B., H.P.S., X.F. and G.C. con-
ducted UV imaging and TEM analysis. E.G.K, C.O.B., A.E.C., and G.C
4. Discussion wrote the paper with contributions from all authors.

Successful liquid injector-based SFX experiments require

consistent delivery of well diffracting single crystals into the XFEL
beam path. The inherent diffraction quality of the microcrystals,
This work was supported by SLAC and Laboratory Directed
crystalline monodispersity and the compatibility of the sample to
Research Development grant 0006-15 (E.G.K. and A.E.C.). Use of the
the injection process are all important factors. Our parallel SFX and
Linac Coherent Light Source (LCLS), SLAC National Accelerator
TEM experiments with HPCD microcrystals illustrate that the use of
Laboratory, is supported by the U.S. Department of Energy, Ofce of
optimized samples with the GDVN injector, such as the ordered
Science, and Ofce of Basic Energy Sciences under Contract No. DE-
monodispersed H200Q variant microcrystals, will result in efcient
AC02-76SF00515. Use of the Stanford Synchrotron Radiation
SFX experiments. While not reported herein, approximately 16 min
Lightsource, SLAC National Accelerator Laboratory, is supported by
of protein crystal screening time at CXI (LCLS) resulted in an
the U.S. Department of Energy, Ofce of Science, Ofce of Basic
enzyme structure at 1.75 resolution, which is one of the most
Energy Sciences under Contract No. DE-AC02-76SF00515. The SSRL
rapidly collected SFX datasets at atomic resolution using a GDVN
Structural Molecular Biology Program is supported by the DOE
injector (manuscript in preparation). In contrast, the presence of
Ofce of Biological and Environmental Research, and by the Na-
protein aggregates or crystal conglomerates can greatly decrease
tional Institutes of Health, National Institute of General Medical
the occurrence of useful diffraction images (even if the crystal lat-
Sciences (including P41GM103393). The contents of this publica-
tice is of high quality), requiring much longer data collection time
tion are solely the responsibility of the authors and do not neces-
and increased sample volumes to acquire enough data for a com-
sarily represent the ofcial views of NIGMS or NIH. We thank
plete dataset. Therefore, pre-characterization of samples to identify
Michael M. Mbughuni for protein purication, and staff at LCLS-CXI
and optimize conditions that promote monodispersity with highly
for assistance with data collection. This work was supported by the
ordered crystal lattices prior to XFEL beam time would lead to
National Institute of General Medical Sciences of the US National
increased efciency and higher-quality SFX data.
Institutes of Health (NIH) under Award numbers GM112686 (G.C),
The application of TEM is particularly advantageous in this re-
GM112497 (C.O.B), and GM102520 (A. S. B.). H.P.S and G.C
gard, for systems where crystals are too small (<5 mm) for X-ray
acknowledge support from BioXFEL-STC1231306.
diffraction screening measurements at micro-focused synchrotron
beamlines. X-ray powder diffraction (XPD) is a commonly used tool
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