Experiment: 6VN4

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		In House Model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		277	NULL

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.38	α = 90
b = 70.715	β = 93.4
c = 78.551	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	PIXEL	DECTRIS PILATUS 6M		2016-05-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9999	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	2.69	78.41	94.4	0.037	0.045	0.999	12.86	3		21844			75.078

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.69	2.94	98.1		0.449	0.55	0.937	2.72	3

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	In House Model	2.69	44	21120	724	94.46	0.2443	0.2422	0.25	0.2999	0.31	RANDOM	79.728

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]
-0.21		0.57	-1.16		1.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.013
r_dihedral_angle_4_deg	17.666
r_dihedral_angle_3_deg	15.199
r_dihedral_angle_1_deg	7.081
r_angle_refined_deg	1.731
r_angle_other_deg	1.311
r_chiral_restr	0.092
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.013
r_dihedral_angle_4_deg	17.666
r_dihedral_angle_3_deg	15.199
r_dihedral_angle_1_deg	7.081
r_angle_refined_deg	1.731
r_angle_other_deg	1.311
r_chiral_restr	0.092
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.005
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5541
Nucleic Acid Atoms
Solvent Atoms	25
Heterogen Atoms	60

Software

Software
Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
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.