9BPY | pdb_00009bpy

Human PARP1 ART domain bound to NAD+ analogs benzamide adenine dinucleotide and carba-NAD+


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP295PARP1 ART (30 mg/ml) was crystallized in the presence of 1.6 mM BAD in 24 to 29% PEG 3350, 0.2 M NaCl, 0.1 M Bis-Tris pH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.3146.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.664α = 98.49
b = 74.142β = 105.16
c = 85.182γ = 104.8
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2024-03-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08B1-11.18CLSI08B1-1

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
12.819.9597.90.0880.0990.0440.99812.44.923920
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)
12.82.9597.31.3141.4750.6610.6084.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.819.9522735118297.860.225880.224280.22350.257580.2575RANDOM100.99
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]
-3.230.32-0.141.461.120.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.217
r_dihedral_angle_2_deg8.002
r_dihedral_angle_1_deg6.748
r_long_range_B_refined5.424
r_long_range_B_other5.424
r_mcangle_it3.246
r_mcangle_other3.246
r_scangle_other2.681
r_mcbond_other1.876
r_mcbond_it1.875
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.217
r_dihedral_angle_2_deg8.002
r_dihedral_angle_1_deg6.748
r_long_range_B_refined5.424
r_long_range_B_other5.424
r_mcangle_it3.246
r_mcangle_other3.246
r_scangle_other2.681
r_mcbond_other1.876
r_mcbond_it1.875
r_scbond_it1.514
r_scbond_other1.514
r_angle_refined_deg0.882
r_angle_other_deg0.297
r_chiral_restr0.039
r_bond_refined_d0.003
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7422
Nucleic Acid Atoms
Solvent Atoms10
Heterogen Atoms220

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction