Experiment: 6VRI

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	294	1.6 M ammonium sulfate, 0.1 M MES, pH 4.5, supplemented with 5% w/v n-Dodecyl-b-D-maltoside

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.416	α = 90
b = 68.416	β = 90
c = 217.748	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	CCD	MARMOSAIC 225 mm CCD		2018-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.94	59.25	99.5	0.15	0.051	8.1	9		44856			30.626

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.94	1.97	86.2		1.627	0.534	2.1	8.9

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1QWD	1.94	59.25	42637	2141	99.31	0.2139	0.2121	0.2494	RANDOM	32.65

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]
-0.11	-0.05		-0.11		0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.376
r_dihedral_angle_4_deg	16.624
r_dihedral_angle_3_deg	15.13
r_dihedral_angle_1_deg	7.516
r_mcangle_it	4.003
r_mcbond_it	2.933
r_mcbond_other	2.895
r_angle_other_deg	2.361
r_angle_refined_deg	1.705
r_chiral_restr	0.078

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.376
r_dihedral_angle_4_deg	16.624
r_dihedral_angle_3_deg	15.13
r_dihedral_angle_1_deg	7.516
r_mcangle_it	4.003
r_mcbond_it	2.933
r_mcbond_other	2.895
r_angle_other_deg	2.361
r_angle_refined_deg	1.705
r_chiral_restr	0.078
r_bond_other_d	0.035
r_gen_planes_other	0.018
r_bond_refined_d	0.01
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3707
Nucleic Acid Atoms
Solvent Atoms	72
Heterogen Atoms	108

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
xia2	data reduction

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.