Experiment: 8GKP

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION		289	polyethyleneglycol 550 monomethylether, polyethyleneglycol 20,000, MES/Imidazole

Crystal Properties
Matthews coefficient	Solvent content
1.96	41.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.092	α = 90
b = 75.218	β = 101.39
c = 87.929	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	Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2	2021-10-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.97946	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.55	86.197	97.3	0.064	0.074	0.037	10.9	3.9	91847	91847

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.63	95.6		0.945	0.945	1.099	0.553	0.8	3.8

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	1.55	30.2	87267	4546	97.08	0.1556	0.1529	0.15	0.2065	0.21	RANDOM	24.11

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]
0.5		-0.09	0.08		-0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.779
r_sphericity_free	22.578
r_dihedral_angle_4_deg	18.082
r_dihedral_angle_3_deg	13.73
r_sphericity_bonded	11.662
r_dihedral_angle_1_deg	6.189
r_rigid_bond_restr	3.309
r_angle_refined_deg	1.515
r_chiral_restr	0.121
r_bond_refined_d	0.013

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.779
r_sphericity_free	22.578
r_dihedral_angle_4_deg	18.082
r_dihedral_angle_3_deg	13.73
r_sphericity_bonded	11.662
r_dihedral_angle_1_deg	6.189
r_rigid_bond_restr	3.309
r_angle_refined_deg	1.515
r_chiral_restr	0.121
r_bond_refined_d	0.013
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5542
Nucleic Acid Atoms
Solvent Atoms	414
Heterogen Atoms	68

Software

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