3KJD

Human poly(ADP-ribose) polymerase 2, catalytic fragment in complex with an inhibitor ABT-888

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	25% PEG 3350, 0.1M Tris, 0.25M NaCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.134	α = 90
b = 134.611	β = 117.68
c = 58.314	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	ADSC QUANTUM 315	mirrors	2009-09-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9789	Diamond	I04

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	1.95	41	99.3	0.096	0.125	11.5	3.8	57455	57455

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)
1	1.95	2	99.7		0.568	0.582	2.7	3.8	4253

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 3KCZ	1.95	40.97	54581	54581	2873	100	0.18157	0.18157	0.17889	0.23192	RANDOM	18.149

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]
0.44		0.29	0.18		-0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.663
r_dihedral_angle_4_deg	18.662
r_dihedral_angle_3_deg	13.772
r_dihedral_angle_1_deg	6.102
r_scangle_it	4.334
r_scbond_it	2.661
r_mcangle_it	1.665
r_angle_refined_deg	1.488
r_angle_other_deg	0.919
r_mcbond_it	0.912
r_mcbond_other	0.236
r_chiral_restr	0.092
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5562
Nucleic Acid Atoms
Solvent Atoms	490
Heterogen Atoms	48

Software

Software
Software Name	Purpose
DNA	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling