Experiment: 5VP7

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4I8G

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		295	0.2 mol L-1 sodium acetate, 0.1 mol L-1 Tris pH 8.5, 26% PEG 3,350

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.773	α = 90
b = 93.773	β = 90
c = 119.918	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		2016-11-29	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	1.7	28.12	99.9	0.082	0.082	0.09	0.038	0.998	10.8	5.7	43235	43235

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	1.7	1.79	100		0.873	0.033	0.037	0.016	0.729		5.6	6314

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	4I8G	1.7	27.07	40983	2251	99.91	0.1727	0.1709	0.18	0.2067	0.22	RANDOM	30.481

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]
-0.79	-0.4		-0.79		2.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.264
r_dihedral_angle_4_deg	18.651
r_dihedral_angle_3_deg	12.143
r_dihedral_angle_1_deg	6.206
r_angle_refined_deg	1.615
r_angle_other_deg	0.793
r_chiral_restr	0.1
r_bond_refined_d	0.014
r_gen_planes_refined	0.012
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.264
r_dihedral_angle_4_deg	18.651
r_dihedral_angle_3_deg	12.143
r_dihedral_angle_1_deg	6.206
r_angle_refined_deg	1.615
r_angle_other_deg	0.793
r_chiral_restr	0.1
r_bond_refined_d	0.014
r_gen_planes_refined	0.012
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2722
Nucleic Acid Atoms
Solvent Atoms	201
Heterogen Atoms	70

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
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.