Experiment: 6VG5

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	291	3.0 M NaNO3, 100 mM HEPES pH 6.8, 5% glycerol

Crystal Properties
Matthews coefficient	Solvent content
1.87	34.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.4	α = 90
b = 25.5	β = 92.55
c = 68.5	γ = 90

Symmetry
Space Group	P 1 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		2018-03-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.07812	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)	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	1.5	50	93.4	0.094	0.103	0.042	8.7	6.1		21285

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	1.5	1.53	75.9		0.829	0.91	0.369	0.695		5.8

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	1sfk	1.5	40.39	19240	973	88.57	0.1478	0.1454	0.1937	RANDOM	17.535

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]
0.16		-0.07	-0.05		-0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.452
r_dihedral_angle_3_deg	12.335
r_dihedral_angle_4_deg	12.07
r_dihedral_angle_1_deg	4.847
r_mcangle_it	2.124
r_angle_refined_deg	1.629
r_mcbond_it	1.585
r_mcbond_other	1.582
r_angle_other_deg	1.323
r_rigid_bond_restr	1.102

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.452
r_dihedral_angle_3_deg	12.335
r_dihedral_angle_4_deg	12.07
r_dihedral_angle_1_deg	4.847
r_mcangle_it	2.124
r_angle_refined_deg	1.629
r_mcbond_it	1.585
r_mcbond_other	1.582
r_angle_other_deg	1.323
r_rigid_bond_restr	1.102
r_chiral_restr	0.064
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1309
Nucleic Acid Atoms
Solvent Atoms	54
Heterogen Atoms	126

Software

Software
Software Name	Purpose
HKL-2000	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	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 R01GM133198.