4GV2

Human ARTD3 (PARP3) - Catalytic domain in complex with inhibitor ME0354


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3FHBPDB ENTRY 3FHB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72931.7M DL-Malic Acid, 0.1M Bis-tris-propane, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.0640.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.188α = 90
b = 56.784β = 112.66
c = 56.618γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rfocusing mirrors2011-07-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.99190DiamondI04

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
11.83099.20.1060.09114.57.52987629876
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)
11.81.8598.20.6120.483.47.22165

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 3FHB1.828.39283822838214941000.162680.162680.161020.19436RANDOM18.035
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]
0.970.43-0.710.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.751
r_dihedral_angle_4_deg16.688
r_dihedral_angle_3_deg12.787
r_dihedral_angle_1_deg6.466
r_scangle_it4.588
r_scbond_it2.744
r_mcangle_it1.825
r_angle_refined_deg1.644
r_mcbond_it1.028
r_angle_other_deg0.912
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.751
r_dihedral_angle_4_deg16.688
r_dihedral_angle_3_deg12.787
r_dihedral_angle_1_deg6.466
r_scangle_it4.588
r_scbond_it2.744
r_mcangle_it1.825
r_angle_refined_deg1.644
r_mcbond_it1.028
r_angle_other_deg0.912
r_mcbond_other0.282
r_chiral_restr0.098
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.001
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 Atoms2752
Nucleic Acid Atoms
Solvent Atoms178
Heterogen Atoms28

Software

Software
Software NamePurpose
MxCuBEdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling