3HKV

Human poly(ADP-ribose) polymerase 10, catalytic fragment in complex with an inhibitor 3-aminobenzamide

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BLJ	PDB ENTRY 3BLJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	0.49M NaH2PO4, 0.9M K2HPO4, pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.93	58.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.38	α = 90
b = 97.38	β = 90
c = 121.16	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD	Rh-coated Si mirrors	2009-03-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-3	0.97900	MAX II	I911-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	2.1	30	99.6	0.093	0.089	15.3	7.8	34589	34589

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.1	2.15	99.4		0.722	0.428	4	8	2499

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3BLJ	2.1	29.84	32856	32856	1730	100	0.19801	0.19801	0.19574	0.24196	RANDOM	30.7

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]
1.05			1.05		-2.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.76
r_dihedral_angle_4_deg	19.866
r_dihedral_angle_3_deg	16.172
r_dihedral_angle_1_deg	5.882
r_scangle_it	4.628
r_scbond_it	2.691
r_mcangle_it	1.883
r_angle_refined_deg	1.506
r_mcbond_it	0.986
r_angle_other_deg	0.917

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.76
r_dihedral_angle_4_deg	19.866
r_dihedral_angle_3_deg	16.172
r_dihedral_angle_1_deg	5.882
r_scangle_it	4.628
r_scbond_it	2.691
r_mcangle_it	1.883
r_angle_refined_deg	1.506
r_mcbond_it	0.986
r_angle_other_deg	0.917
r_mcbond_other	0.214
r_chiral_restr	0.097
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3086
Nucleic Acid Atoms
Solvent Atoms	183
Heterogen Atoms	37

Software

Software
Software Name	Purpose
MxCuBE	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

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.