6NRJ

Crystal Structure of human PARP-1 ART domain bound to inhibitor UTT93


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6BHVPDBID 6BHV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION7.5298~20% PEG 3350, 0.2 M ammonium sulfate or sodium citrate, 100 mM Hepes pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.5651.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.465α = 90
b = 94.465β = 90
c = 137.627γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2018-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.979CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.6547.981000.0770.0780.015122.727.837738
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.6899.81.7381.7710.3340.74926.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDBID 6BHV1.6547.9835588197599.580.16890.16770.1913RANDOM34.032
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]
0.410.41-0.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.981
r_dihedral_angle_4_deg13.515
r_dihedral_angle_3_deg12.505
r_dihedral_angle_1_deg6.71
r_angle_refined_deg1.262
r_angle_other_deg0.907
r_chiral_restr0.065
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.981
r_dihedral_angle_4_deg13.515
r_dihedral_angle_3_deg12.505
r_dihedral_angle_1_deg6.71
r_angle_refined_deg1.262
r_angle_other_deg0.907
r_chiral_restr0.065
r_bond_refined_d0.009
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 Atoms1895
Nucleic Acid Atoms
Solvent Atoms127
Heterogen Atoms67

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction