Experiment: 7QDJ

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	278	0.1M (Sodium malonate dibasic monohydrate, Imidazole, Boric acid), 25% w/v PEG1500 at pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
1.77	30.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 26.928	α = 90
b = 19.379	β = 96.61
c = 55.644	γ = 90

Symmetry
Space Group	C 1 2/c 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-F		2020-02-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9119	Diamond	I04-1

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	1.44	27.64	97.1	0.032	0.034	1	40.8	13		5150

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	1.44	1.47	94.8		0.097	0.1	1	19.1	13.9

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	AB INITIO PHASING	THROUGHOUT	1.44	15.7	4677	230	96.77	0.1314	0.1295	0.1679	RANDOM	9.84

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]
0.27		-0.21	0.04		-0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.246
r_dihedral_angle_3_deg	9.514
r_rigid_bond_restr	4.807
r_dihedral_angle_1_deg	4.561
r_angle_refined_deg	3.229
r_angle_other_deg	1.463
r_chiral_restr	0.16
r_bond_refined_d	0.026
r_gen_planes_refined	0.009
r_bond_other_d	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.246
r_dihedral_angle_3_deg	9.514
r_rigid_bond_restr	4.807
r_dihedral_angle_1_deg	4.561
r_angle_refined_deg	3.229
r_angle_other_deg	1.463
r_chiral_restr	0.16
r_bond_refined_d	0.026
r_gen_planes_refined	0.009
r_bond_other_d	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	145
Nucleic Acid Atoms
Solvent Atoms	27
Heterogen Atoms	15

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXT	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.