Experiment: 8WV8

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7DYJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	7	313	sodium/pottasium tartrae, sodium acetate, KCl

Crystal Properties
Matthews coefficient	Solvent content
	40.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.191	α = 90
b = 95.191	β = 90
c = 184.086	γ = 120

Symmetry
Space Group	P 63

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M		2020-07-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9	SPring-8	BL44XU

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	2.93	49.22	99.7	0.117	15.8	10.3		20257

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.93	3.03			0.913

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	2.93	49.22	19328	939	99.79	0.2783	0.2755	0.28	0.3351	0.32	RANDOM	71.374

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]
-4.57	-2.28		-4.57		14.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.985
r_dihedral_angle_3_deg	25.469
r_dihedral_angle_4_deg	22.097
r_dihedral_angle_1_deg	2.944
r_angle_refined_deg	1.234
r_angle_other_deg	1.123
r_chiral_restr	0.029
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.985
r_dihedral_angle_3_deg	25.469
r_dihedral_angle_4_deg	22.097
r_dihedral_angle_1_deg	2.944
r_angle_refined_deg	1.234
r_angle_other_deg	1.123
r_chiral_restr	0.029
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6510
Nucleic Acid Atoms
Solvent Atoms	16
Heterogen Atoms	128

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
MOLREP	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.