4L7O

Human artd3 (parp3) - catalytic domain in complex with inhibitor STO1542


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4GV4PDB ENTRY 4GV4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72931.8M DL-Malic Acid, 0.1M Bis-tris-propane , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0540.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.519α = 90
b = 56.918β = 112.43
c = 56.84γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2011-07-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97950DiamondI04

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
123099.70.1260.12215.97.42188821888
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)
122.0599.60.6740.4753.77.51601

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 4GV4228.46207932079310951000.16520.16520.162770.20996RANDOM19.446
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]
1.20.2-0.94-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.713
r_dihedral_angle_4_deg18.257
r_dihedral_angle_3_deg14.364
r_dihedral_angle_1_deg6.318
r_scangle_it4.556
r_scbond_it2.784
r_mcangle_it1.876
r_angle_refined_deg1.677
r_mcbond_it1.036
r_angle_other_deg0.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.713
r_dihedral_angle_4_deg18.257
r_dihedral_angle_3_deg14.364
r_dihedral_angle_1_deg6.318
r_scangle_it4.556
r_scbond_it2.784
r_mcangle_it1.876
r_angle_refined_deg1.677
r_mcbond_it1.036
r_angle_other_deg0.98
r_mcbond_other0.263
r_chiral_restr0.103
r_bond_refined_d0.019
r_gen_planes_refined0.008
r_bond_other_d0.003
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 Atoms2755
Nucleic Acid Atoms
Solvent Atoms135
Heterogen Atoms33

Software

Software
Software NamePurpose
GDAdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling