Experiment: 7VDS

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	291	0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.06	α = 90
b = 118.06	β = 90
c = 153.69	γ = 120

Symmetry
Space Group	P 32 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 EIGER X 9M		2020-02-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.12713	APS	21-ID-D

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	3.05	48.51	100	0.144	0.149	0.035	0.999	14.3	18.1		24161

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	3.05	3.26	100		2.565	2.636	0.605	0.565		18.6

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	3O0G	3.05	48.51	22918	1207	99.9	0.2279	0.2254	0.2715	RANDOM	133.419

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]
-0.14	-0.07		-0.14		0.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.246
r_dihedral_angle_4_deg	16.62
r_dihedral_angle_3_deg	15.435
r_dihedral_angle_1_deg	6.043
r_angle_refined_deg	1.244
r_angle_other_deg	1.048
r_chiral_restr	0.047
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.246
r_dihedral_angle_4_deg	16.62
r_dihedral_angle_3_deg	15.435
r_dihedral_angle_1_deg	6.043
r_angle_refined_deg	1.244
r_angle_other_deg	1.048
r_chiral_restr	0.047
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6954
Nucleic Acid Atoms
Solvent Atoms	69
Heterogen Atoms	183

Software

Software
Software Name	Purpose
Aimless	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 R01GM133198.