Experiment: 7PXR

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5ACH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	3.5	298	3.0 M sodium chloride, 0.1 M citric acid pH 3.5 The crystals were soaked in a drop containing 3.0 M sodium chloride, 0.1 M citric acid pH 5.5 for 10 min before mounting

Crystal Properties
Matthews coefficient	Solvent content
3.35	63.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 126.659	α = 90
b = 126.659	β = 90
c = 126.659	γ = 90

Symmetry
Space Group	P 41 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	PIXEL	DECTRIS EIGER R 4M		2019-08-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.540

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.8	29.87	100	0.047	1	43.8	17.2		32798

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.84	100		0.509	0.925	4.8	10.2

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	5ACH	1.8	29.87	31034	1670	99.95	0.1478	0.1467	0.16	0.1662	0.18	RANDOM	20.874

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.262
r_dihedral_angle_4_deg	15.122
r_dihedral_angle_3_deg	11.782
r_dihedral_angle_1_deg	6.979
r_angle_refined_deg	1.844
r_angle_other_deg	1.478
r_chiral_restr	0.096
r_bond_refined_d	0.014
r_gen_planes_refined	0.012
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.262
r_dihedral_angle_4_deg	15.122
r_dihedral_angle_3_deg	11.782
r_dihedral_angle_1_deg	6.979
r_angle_refined_deg	1.844
r_angle_other_deg	1.478
r_chiral_restr	0.096
r_bond_refined_d	0.014
r_gen_planes_refined	0.012
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1788
Nucleic Acid Atoms
Solvent Atoms	182
Heterogen Atoms	28

Software

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