6V3W | pdb_00006v3w

Human Poly(ADP-Ribose) Polymerase 12, Catalytic fragment with four point mutations in complex with RBN-2397

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PQF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	291.15	0.2 M Ammonium acetate, 0.1 M Sodium acetate pH 4, 15% w/v PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.95	58.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.466	α = 90
b = 80.466	β = 90
c = 142.648	γ = 120

Symmetry
Space Group	P 65 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	63	PIXEL	DECTRIS EIGER2 X 16M		2018-07-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.97918	SSRF	BL17U1

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	2.04	69.78	99.2	0.093	0.096	0.022	0.998	18.8	19.3		18026

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	2.04	2.15	98.3		1.636	1.681	0.384	0.903		18.8

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 (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2PQF	2.04	69.78	17084	918	98.84	0.2127	0.2104	0.2553	RANDOM	61.258

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]
0.97	0.49		0.97		-3.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.462
r_dihedral_angle_4_deg	27.99
r_dihedral_angle_3_deg	15.241
r_dihedral_angle_1_deg	7.106
r_angle_refined_deg	1.592
r_angle_other_deg	1.353
r_chiral_restr	0.071
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_gen_planes_other	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.462
r_dihedral_angle_4_deg	27.99
r_dihedral_angle_3_deg	15.241
r_dihedral_angle_1_deg	7.106
r_angle_refined_deg	1.592
r_angle_other_deg	1.353
r_chiral_restr	0.071
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1497
Nucleic Acid Atoms
Solvent Atoms	49
Heterogen Atoms	37

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	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 R01GM157729.