Experiment: 6X2D

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VRT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	292	Protein: 7.9 mg/ml, 0.01M Tris pH 8.3; Screen: PACT (F3), 0.2M Sodium iodide, 0.1M Bis-Tris propane pH 6.5, 20% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.614	α = 90
b = 58.812	β = 108.16
c = 47.046	γ = 90

Symmetry
Space Group	P 1 21 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 300 mm CCD	Be	2020-03-17	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)	R Merge I (Observed)	R Sym 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	1.85	30	99.4	0.088	0.088	0.097	0.041	0.985	21.9	5.7		17863		-3	34.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.88	100		0.759	0.759	0.833	0.339	0.927	4.7	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	2vrt	1.85	29.41	16959	887	98.9	0.2085	0.2067	0.2429	RANDOM	43.735

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]
2.65		1.64	-1.57		-1.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	18.204
r_dihedral_angle_4_deg	10.434
r_dihedral_angle_3_deg	9.084
r_dihedral_angle_1_deg	2.049
r_angle_refined_deg	1.292
r_angle_other_deg	0.41
r_chiral_restr	0.057
r_gen_planes_refined	0.05
r_gen_planes_other	0.044
r_bond_refined_d	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	18.204
r_dihedral_angle_4_deg	10.434
r_dihedral_angle_3_deg	9.084
r_dihedral_angle_1_deg	2.049
r_angle_refined_deg	1.292
r_angle_other_deg	0.41
r_chiral_restr	0.057
r_gen_planes_refined	0.05
r_gen_planes_other	0.044
r_bond_refined_d	0.005
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1709
Nucleic Acid Atoms
Solvent Atoms	75
Heterogen Atoms	9

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
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.