Experiment: 5VPY

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
2.68	54.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.609	α = 90
b = 94.609	β = 90
c = 120.808	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	67.81	99.9	0.136	0.136	0.151	0.065	0.993	7.7	5.3		27195

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	2.11	100		0.792	0.047	0.053	0.023	0.613		5.2

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2	67.81	25742	1441	99.78	0.1902	0.1879	0.2	0.2326	0.24	RANDOM	26.994

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]
-0.56	-0.28		-0.56		1.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.178
r_dihedral_angle_4_deg	18.178
r_dihedral_angle_3_deg	14.992
r_dihedral_angle_1_deg	6.665
r_angle_refined_deg	1.585
r_angle_other_deg	0.821
r_chiral_restr	0.1
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.178
r_dihedral_angle_4_deg	18.178
r_dihedral_angle_3_deg	14.992
r_dihedral_angle_1_deg	6.665
r_angle_refined_deg	1.585
r_angle_other_deg	0.821
r_chiral_restr	0.1
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2504
Nucleic Acid Atoms
Solvent Atoms	130
Heterogen Atoms	79

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 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.