Experiment: 7B7S

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	80% Morpheus condition 35 containing: 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 and 20% of JCSG+ condition 59 containing: 14.4 % w/v PEG 8,000, 20% v/v Glycerol, 0.16 M calcium acetate, 0.08 M sodium cacodylate pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
3.19	61.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.077	α = 90
b = 164.7	β = 106.28
c = 73.411	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	PIXEL	DECTRIS PILATUS 6M		2020-06-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.918	BESSY	14.1

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	2.54	47.1	84	0.309	0.342	0.968	5.35	5.502		43971			35.409

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	2.54	2.7	69.2		1.429	1.599	0.468	1	4.762

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	2.54	47.1	41850	2129	84.07	0.2482	0.246	0.2906	RANDOM	37.521

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]
6		2.37	-3.52		-3.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.587
r_dihedral_angle_4_deg	17.018
r_dihedral_angle_3_deg	16.232
r_dihedral_angle_1_deg	6.606
r_angle_other_deg	2.246
r_angle_refined_deg	1.623
r_chiral_restr	0.07
r_bond_other_d	0.034
r_bond_refined_d	0.011
r_gen_planes_other	0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.587
r_dihedral_angle_4_deg	17.018
r_dihedral_angle_3_deg	16.232
r_dihedral_angle_1_deg	6.606
r_angle_other_deg	2.246
r_angle_refined_deg	1.623
r_chiral_restr	0.07
r_bond_other_d	0.034
r_bond_refined_d	0.011
r_gen_planes_other	0.009
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8729
Nucleic Acid Atoms
Solvent Atoms	77
Heterogen Atoms	73

Software

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

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.