Experiment: 8A7R

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8A6U

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.1 M MES, 0.2 CaCl2, 30% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.01	α = 90
b = 78.39	β = 101.85
c = 88.02	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 EIGER X 16M		2020-02-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0	SLS	X06SA

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	30	96.2	0.099	6.9	3.8		51160

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.1	98.6		0.551	2.4

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	8A6U	2	15	48480	2551	96.01	0.1887	0.1866	0.2295	RANDOM	34.131

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]
-2.87		-1.46	-1.48		4.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.172
r_dihedral_angle_3_deg	15.821
r_dihedral_angle_4_deg	15.703
r_dihedral_angle_1_deg	5.258
r_angle_refined_deg	1.189
r_angle_other_deg	1.159
r_rigid_bond_restr	0.615
r_chiral_restr	0.056
r_gen_planes_refined	0.003
r_bond_refined_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.172
r_dihedral_angle_3_deg	15.821
r_dihedral_angle_4_deg	15.703
r_dihedral_angle_1_deg	5.258
r_angle_refined_deg	1.189
r_angle_other_deg	1.159
r_rigid_bond_restr	0.615
r_chiral_restr	0.056
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5307
Nucleic Acid Atoms
Solvent Atoms	130
Heterogen Atoms	41

Software

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