Experiment: 7K95

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.7	293	0.1 M sodium malonate, 16% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.04	α = 90
b = 79.04	β = 90
c = 48.662	γ = 120

Symmetry
Space Group	P 64

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 16M		2019-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.9792	APS	24-ID-C

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	1.9	48.66	100	0.046	0.048	0.013	1	30.9	12.6		13793

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	1.9	1.94	99.9		0.874	0.917	0.788		10.9

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	SAD	THROUGHOUT	1.9	39.55	13086	690	99.91	0.1811	0.1793	0.2092	RANDOM	52.784

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]
0.2	0.1		0.2		-0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.479
r_dihedral_angle_3_deg	16.798
r_dihedral_angle_4_deg	16.393
r_dihedral_angle_1_deg	7.088
r_angle_refined_deg	1.984
r_angle_other_deg	1.434
r_chiral_restr	0.083
r_bond_refined_d	0.015
r_gen_planes_refined	0.013
r_bond_other_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.479
r_dihedral_angle_3_deg	16.798
r_dihedral_angle_4_deg	16.393
r_dihedral_angle_1_deg	7.088
r_angle_refined_deg	1.984
r_angle_other_deg	1.434
r_chiral_restr	0.083
r_bond_refined_d	0.015
r_gen_planes_refined	0.013
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1043
Nucleic Acid Atoms
Solvent Atoms	82
Heterogen Atoms	2

Software

Software
Software Name	Purpose
XDS	data reduction
Aimless	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.