Experiment: 6TV7

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3EK4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		292	0.21 M sodium formate, 0.1 M Bis-Tris-Propane buffer pH 8.5, 18% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.65	66.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.67	α = 90
b = 120.67	β = 90
c = 96.02	γ = 90

Symmetry
Space Group	P 41 21 2

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 2M		2019-11-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	0.999995	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.9	50	100	0.996	11.17	13		16254			55.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	2.98			0.641	1.6

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	3ek4	2.9	47.09	15423	831	99.95	0.1855	0.182	0.2504	RANDOM	55.852

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]
1.61			1.61		-3.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.222
r_dihedral_angle_3_deg	21.168
r_dihedral_angle_4_deg	20.352
r_dihedral_angle_1_deg	8.439
r_angle_refined_deg	1.897
r_angle_other_deg	1.272
r_chiral_restr	0.069
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.222
r_dihedral_angle_3_deg	21.168
r_dihedral_angle_4_deg	20.352
r_dihedral_angle_1_deg	8.439
r_angle_refined_deg	1.897
r_angle_other_deg	1.272
r_chiral_restr	0.069
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3167
Nucleic Acid Atoms
Solvent Atoms	89
Heterogen Atoms	9

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
MOLREP	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.