4QX2 | pdb_00004qx2

Cry3A Toxin structure obtained by injecting Bacillus thuringiensis cells in an XFEL beam, collecting data by serial femtosecond crystallographic methods and processing data with the cctbx.xfel software suite

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DLC	PDB ENTRY 1DLC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	IN VIVO CRYSTALLIZATION		303	Cry3A crystallized within the bacterial cell, IN VIVO CRYSTALLIZATION, temperature 303K

Crystal Properties
Matthews coefficient	Solvent content
3.11	60.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.05	α = 90
b = 134.76	β = 90
c = 104.85	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	PIXEL	Cornell-SLAC Pixel Array Detector (CSPAD)		2013-03-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SLAC LCLS BEAMLINE CXI	1.457	SLAC LCLS	CXI

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.9	52.42	92.3	0.216	59.2	252.5	18583	18583			30.55

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	2.99	39.2		0.906	2.3	1.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 1DLC	2.9	52.42	18583	18583	931	99.14	0.1699	0.1683	0.19	0.2013	0.23	RANDOM	38.39

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.6597			1.3849		-2.0446

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	18.95
t_omega_torsion	2.52
t_angle_deg	0.99
t_bond_d	0.01
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4659
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
cctbx.xfel	data reduction
BUSTER	refinement

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.