Experiment: 7VDU

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GZ8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	277	12% (w/v) PEG 3350, 0.10 M MES pH=7.00

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.851	α = 90
b = 73.035	β = 90
c = 70.731	γ = 90

Symmetry
Space Group	P 21 21 21

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		2018-08-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.999891638756	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	1.53	50.81	98.6	0.055	14.57	4.1		42212

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.53	1.78	99.4		0.517	3.47	4.2

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	MOLECULAR REPLACEMENT	THROUGHOUT	1GZ8	1.53	50.81	38061	4150	98.63	0.1804	0.1764	0.19	0.2175	0.22	RANDOM	24.955

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]
-0.02			-0.35		0.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.053
r_sphericity_free	17.305
r_dihedral_angle_3_deg	13.196
r_dihedral_angle_4_deg	12.592
r_dihedral_angle_1_deg	5.459
r_sphericity_bonded	5.402
r_rigid_bond_restr	3.948
r_angle_other_deg	1.7
r_angle_refined_deg	1.45
r_chiral_restr	0.083

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.053
r_sphericity_free	17.305
r_dihedral_angle_3_deg	13.196
r_dihedral_angle_4_deg	12.592
r_dihedral_angle_1_deg	5.459
r_sphericity_bonded	5.402
r_rigid_bond_restr	3.948
r_angle_other_deg	1.7
r_angle_refined_deg	1.45
r_chiral_restr	0.083
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2339
Nucleic Acid Atoms
Solvent Atoms	230
Heterogen Atoms	37

Software

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