Experiment: 8B54

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6GVA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291.15	70%: 10% w/v PEG 4,000, 20% v/v glycerol, 0.03 M NaNO3, 0.03 M Na2HPO4, 0.03 M (NH4)2SO4, 0.1 M Tris/Bicine pH 8.5 30%:0.8 M sodium phosphate monobasic monohydrate, 0.8 M potassium phosphate monobasic, 0.1 M Sodium HEPES, pH7.5

Crystal Properties
Matthews coefficient	Solvent content
3.17	61.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.023	α = 90
b = 134.978	β = 90
c = 163.963	γ = 90

Symmetry
Space Group	P 21 21 21

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 PILATUS 6M		2020-10-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.6	50	99.9	0.988	5.42	13.6		50620			39.44

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	2.6	2.76			0.717	1.01

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	6GVA	2.6	49.56	49156	1460	99.9	0.2344	0.2328	0.2874	RANDOM	39.612

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]
0.07			-0.12		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.726
r_dihedral_angle_4_deg	17.942
r_dihedral_angle_3_deg	14.355
r_dihedral_angle_1_deg	7.033
r_angle_other_deg	2.237
r_angle_refined_deg	1.596
r_chiral_restr	0.071
r_bond_other_d	0.034
r_bond_refined_d	0.011
r_gen_planes_other	0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.726
r_dihedral_angle_4_deg	17.942
r_dihedral_angle_3_deg	14.355
r_dihedral_angle_1_deg	7.033
r_angle_other_deg	2.237
r_angle_refined_deg	1.596
r_chiral_restr	0.071
r_bond_other_d	0.034
r_bond_refined_d	0.011
r_gen_planes_other	0.01
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8828
Nucleic Acid Atoms
Solvent Atoms	314
Heterogen Atoms	98

Software

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

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.