Experiment: 7PK2

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289	0.2 M sodium malonate, 20% w/v polyethylene glycol 3,350, pH 5.0

Crystal Properties
Matthews coefficient	Solvent content
2	38.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.112	α = 90
b = 63.587	β = 90
c = 135.503	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	PIXEL	DECTRIS EIGER2 X 16M		2020-10-15	M	SINGLE WAVELENGTH
2	1	x-ray	45	PIXEL	DECTRIS PILATUS 12M		2021-05-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03
2	SYNCHROTRON	DIAMOND BEAMLINE I23	2.755	Diamond	I23

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	1.25	37.37	97.22	0.043	0.047	0.018	1	16.2	6.8		146947

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	1.25	1.25			0.4	1.18

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.25	37.37	139600	7348	97.21	0.1779	0.1768	0.19	0.1997	0.21	RANDOM	23.2609

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			0.88		-1.22

RMS Deviations
Key	Refinement Restraint Deviation
TORSION ANGLES. PERIOD 2 (DEGREES)	34.109
TORSION ANGLES. PERIOD 4 (DEGREES)	20.582
TORSION ANGLES. PERIOD 3 (DEGREES)	13.853
TORSION ANGLES. PERIOD 1 (DEGREES)	6.521
r_angle_refined_deg	1.754
r_angle_other_deg	1.45
r_chiral_restr	0.092
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
TORSION ANGLES. PERIOD 2 (DEGREES)	34.109
TORSION ANGLES. PERIOD 4 (DEGREES)	20.582
TORSION ANGLES. PERIOD 3 (DEGREES)	13.853
TORSION ANGLES. PERIOD 1 (DEGREES)	6.521
r_angle_refined_deg	1.754
r_angle_other_deg	1.45
r_chiral_restr	0.092
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4588
Nucleic Acid Atoms
Solvent Atoms	433
Heterogen Atoms	14

Software

Software
Software Name	Purpose
xia2	data reduction
XSCALE	data scaling
SHELXD	phasing
CRANK2	phasing
HKL2Map	model building
PHASER	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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.