3C4H

Human poly(ADP-ribose) polymerase 3, catalytic fragment in complex with an inhibitor DR2313


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PA9PDB entry 2PA9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72981.9 M DL-Malic acid, 0.1 M Bis-Tris propane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0640.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.91α = 90
b = 57.33β = 112.36
c = 56.26γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Mirrors2007-09-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID291.0000ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.12099.60.10515.227.4189781897824.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.21000.454.647.52442

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 2PA92.119.9818027180279491000.177580.177580.174210.24197RANDOM25.402
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]
0.290.15-0.190.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.989
r_dihedral_angle_4_deg17.77
r_dihedral_angle_3_deg12.782
r_dihedral_angle_1_deg5.781
r_scangle_it2.201
r_scbond_it1.397
r_angle_refined_deg1.13
r_mcangle_it0.941
r_mcbond_it0.568
r_nbtor_refined0.297
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.989
r_dihedral_angle_4_deg17.77
r_dihedral_angle_3_deg12.782
r_dihedral_angle_1_deg5.781
r_scangle_it2.201
r_scbond_it1.397
r_angle_refined_deg1.13
r_mcangle_it0.941
r_mcbond_it0.568
r_nbtor_refined0.297
r_nbd_refined0.187
r_symmetry_vdw_refined0.187
r_xyhbond_nbd_refined0.132
r_symmetry_hbond_refined0.126
r_chiral_restr0.071
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2769
Nucleic Acid Atoms
Solvent Atoms153
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing