Experiment: 7P8K

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4B6X	4B6X, 5W3X
experimental model	PDB	5W3X	4B6X, 5W3X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.8M Potassium sodium tartrate tertrahydrate, 0.1M Sodium HEPES pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.607	α = 90
b = 105.607	β = 90
c = 66.987	γ = 120

Symmetry
Space Group	P 61 2 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 6M-F		2019-11-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91188	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.65	45.77	99.9	0.095	0.097	0.019	1	17.4	20.8		6800

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	2.65	2.78	100		1.185	1.211	0.238	0.904		21.9

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4B6X, 5W3X	2.65	45.77	6477	299	99.76	0.2473	0.2454	0.2838	RANDOM	93.11

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]
3.25	1.63		3.25		-10.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.638
r_dihedral_angle_4_deg	18.764
r_dihedral_angle_3_deg	15.652
r_dihedral_angle_1_deg	5.585
r_angle_refined_deg	1.237
r_angle_other_deg	1.144
r_chiral_restr	0.049
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.638
r_dihedral_angle_4_deg	18.764
r_dihedral_angle_3_deg	15.652
r_dihedral_angle_1_deg	5.585
r_angle_refined_deg	1.237
r_angle_other_deg	1.144
r_chiral_restr	0.049
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1016
Nucleic Acid Atoms
Solvent Atoms	3
Heterogen Atoms	1

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	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 R01GM133198.