Experiment: 5VRY

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	50 mM imidazole pH 7.0-7.5, 350 mM sodium acetate, 16-18% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.9	α = 90
b = 80.1	β = 107.2
c = 55.6	γ = 90

Symmetry
Space Group	P 1 21 1

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 MX300HE		2015-11-12	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)	Rrim 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	1.9	48.62	96.5	0.05	0.069	0.998	11.11	1.935		63931		-3	30.123

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2.2	98.7		0.234	0.317	0.877	3.36	1.924

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4RPX	1.9	48.62	31519	1659	98.57	0.2048	0.2028	0.2435	RANDOM	27.365

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]
0.02			-0.04		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.361
r_dihedral_angle_4_deg	13.964
r_dihedral_angle_3_deg	13.482
r_dihedral_angle_1_deg	4.883
r_angle_refined_deg	1.148
r_angle_other_deg	1.021
r_chiral_restr	0.072
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.361
r_dihedral_angle_4_deg	13.964
r_dihedral_angle_3_deg	13.482
r_dihedral_angle_1_deg	4.883
r_angle_refined_deg	1.148
r_angle_other_deg	1.021
r_chiral_restr	0.072
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2617
Nucleic Acid Atoms	652
Solvent Atoms	305
Heterogen Atoms	50

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
PHASER	phasing
XDS	data reduction

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.