Experiment: 7PQM

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7PQI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	NULL

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.634	α = 90
b = 48.293	β = 123.85
c = 82.692	γ = 90

Symmetry
Space Group	C 1 2 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 EIGER2 XE 16M		2021-02-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	1.55	43.5	99.9	0.105	0.11	0.033	0.999	8.9	10.9		57543			18.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.58	99		1.55	1.625	0.482	0.66		11.1

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	7PQI	1.55	43.54	54572	2969	99.94	0.1823	0.18	0.2235	RANDOM	31.638

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]
3.33		2.55	-5.57		-0.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.193
r_dihedral_angle_4_deg	14.2
r_dihedral_angle_3_deg	12.364
r_rigid_bond_restr	6.718
r_dihedral_angle_1_deg	5.782
r_angle_other_deg	1.341
r_angle_refined_deg	1.235
r_chiral_restr	0.059
r_bond_refined_d	0.006
r_gen_planes_refined	0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.193
r_dihedral_angle_4_deg	14.2
r_dihedral_angle_3_deg	12.364
r_rigid_bond_restr	6.718
r_dihedral_angle_1_deg	5.782
r_angle_other_deg	1.341
r_angle_refined_deg	1.235
r_chiral_restr	0.059
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.005
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2892
Nucleic Acid Atoms
Solvent Atoms	354
Heterogen Atoms	65

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
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.