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)
TypeSourceAccession CodeDetails
experimental modelPDB 3BLJPDB ENTRY 3BLJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52770.49M NaH2PO4, 0.9M K2HPO4, pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.9358.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.38α = 90
b = 97.38β = 90
c = 121.16γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDRh-coated Si mirrors2009-03-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-30.97900MAX III911-3

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.13099.60.0930.08915.37.83458934589
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)
2.12.1599.40.7220.428482499

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 3BLJ2.129.84328563285617301000.198010.198010.195740.24196RANDOM30.7
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]
1.051.05-2.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.76
r_dihedral_angle_4_deg19.866
r_dihedral_angle_3_deg16.172
r_dihedral_angle_1_deg5.882
r_scangle_it4.628
r_scbond_it2.691
r_mcangle_it1.883
r_angle_refined_deg1.506
r_mcbond_it0.986
r_angle_other_deg0.917
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.76
r_dihedral_angle_4_deg19.866
r_dihedral_angle_3_deg16.172
r_dihedral_angle_1_deg5.882
r_scangle_it4.628
r_scbond_it2.691
r_mcangle_it1.883
r_angle_refined_deg1.506
r_mcbond_it0.986
r_angle_other_deg0.917
r_mcbond_other0.214
r_chiral_restr0.097
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3086
Nucleic Acid Atoms
Solvent Atoms183
Heterogen Atoms37

Software

Software
Software NamePurpose
MxCuBEdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling