Experiment: 5VQ8

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		295	0.2 mol/L sodium acetate, 0.1 mol/L Tris pH 8.5, 24% PEG 3,350

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.9	α = 90
b = 93.9	β = 90
c = 120.562	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RAYONIX MX225HE		2017-04-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97931	APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.3	67.42	99.8	0.101	0.101	0.111	0.047	0.997	12.4	5.7	17602	17602

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.42	100		0.684	0.032	0.035	0.016	0.71		5.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.3	67.42	16635	940	99.63	0.2201	0.2174	0.266	RANDOM	41.756

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]
-0.42	-0.21		-0.42		1.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.257
r_dihedral_angle_4_deg	15.379
r_dihedral_angle_3_deg	15.118
r_dihedral_angle_1_deg	7.069
r_angle_refined_deg	0.942
r_angle_other_deg	0.602
r_chiral_restr	0.069
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.257
r_dihedral_angle_4_deg	15.379
r_dihedral_angle_3_deg	15.118
r_dihedral_angle_1_deg	7.069
r_angle_refined_deg	0.942
r_angle_other_deg	0.602
r_chiral_restr	0.069
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2504
Nucleic Acid Atoms
Solvent Atoms	34
Heterogen Atoms	58

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
PHASER	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.