3KCZ

Human poly(ADP-ribose) polymerase 2, catalytic fragment in complex with an inhibitor 3-aminobenzamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GS0PDB ENTRY 1GS0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP927722% PEG 3350, 0.1M Tris-HCl, 0.01M 3-aminobenzamide, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4249.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.28α = 90
b = 134.72β = 117.67
c = 58.25γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2009-09-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97890DiamondI04

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
124599.10.1120.1610.13.1533275332718.1
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)RedundancyNumber Unique Reflections (All)
122.0599.40.5480.6382.93.13893

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1GS0240.97506595065926671000.189910.189910.187430.23665RANDOM15.693
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]
0.540.40.05-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.738
r_dihedral_angle_4_deg20.153
r_dihedral_angle_3_deg14.104
r_dihedral_angle_1_deg5.78
r_scangle_it3.731
r_scbond_it2.267
r_mcangle_it1.428
r_angle_refined_deg1.362
r_angle_other_deg0.877
r_mcbond_it0.769
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.738
r_dihedral_angle_4_deg20.153
r_dihedral_angle_3_deg14.104
r_dihedral_angle_1_deg5.78
r_scangle_it3.731
r_scbond_it2.267
r_mcangle_it1.428
r_angle_refined_deg1.362
r_angle_other_deg0.877
r_mcbond_it0.769
r_mcbond_other0.179
r_chiral_restr0.081
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms5563
Nucleic Acid Atoms
Solvent Atoms387
Heterogen Atoms32

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling