Experiment: 8K4R

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	HEPES-Na, sodium citrate

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.501	α = 94.18
b = 72.987	β = 90.87
c = 80.209	γ = 103.34

Symmetry
Space Group	P 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 PILATUS3 S 6M		2022-05-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0	Photon Factory	BL-5A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.3	50	97.9	0.049	0.999	11.2	3.5		54087

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.37	97.3		0.626	0.826	1.6	3.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.3	46.04	51384	2703	97.91	0.2089	0.2067	0.2508	RANDOM	62.016

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]
0.94	0.57	-1.12	-0.65	-0.62	-0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.535
r_dihedral_angle_4_deg	19.119
r_dihedral_angle_3_deg	17.3
r_dihedral_angle_1_deg	7.152
r_angle_other_deg	1.639
r_angle_refined_deg	1.445
r_chiral_restr	0.063
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.535
r_dihedral_angle_4_deg	19.119
r_dihedral_angle_3_deg	17.3
r_dihedral_angle_1_deg	7.152
r_angle_other_deg	1.639
r_angle_refined_deg	1.445
r_chiral_restr	0.063
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8624
Nucleic Acid Atoms
Solvent Atoms	43
Heterogen Atoms	58

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
MOLREP	phasing
Coot	model building

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 R01GM133198.