Experiment: 7QDK

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	293	0.12 M (0.2M 1,6-Hexanediol; 0.2M 1-Butanol; 0.2M 1,2-Propanediol; 0.2M 2-Propanol; 0.2M 1,4-Butanediol; 0.2M 1,3-Propanediol),0.1 M (Imidazole; MES monohydrate (acid)), 37.5 % v/v (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350) at pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
1.83	32.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 22.22	α = 90
b = 22.22	β = 90
c = 128.32	γ = 120

Symmetry
Space Group	P 31

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 EIGER2 XE 16M		2020-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.919	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.41	21.39	100	0.071	1	21.5	9.9		13714

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.41	1.43			0.566	0.9	2.9	6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	AB INITIO PHASING	THROUGHOUT	1.41	19.25	12996	660	99.87	0.1404	0.1388	0.1765	RANDOM	20.276

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]
-0.35	-0.17		-0.35		1.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.422
r_dihedral_angle_3_deg	13.921
r_dihedral_angle_1_deg	2.796
r_angle_other_deg	1.4
r_rigid_bond_restr	1.379
r_angle_refined_deg	1.297
r_chiral_restr	0.06
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.422
r_dihedral_angle_3_deg	13.921
r_dihedral_angle_1_deg	2.796
r_angle_other_deg	1.4
r_rigid_bond_restr	1.379
r_angle_refined_deg	1.297
r_chiral_restr	0.06
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	686
Nucleic Acid Atoms
Solvent Atoms	91
Heterogen Atoms	17

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Arcimboldo	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.