4L7N

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 DROP72931.7M DL-Malic Acid, 0.1M Bis-tris-propane , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0539.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.945α = 90
b = 56.822β = 112.41
c = 56.427γ = 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
11.83099.70.0970.10417.77.42991729917
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)
11.81.8598.70.8080.6062.87.22168

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 4GV41.828.41284212842114961000.160270.160270.158250.1981RANDOM19.799
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]
0.770.11-0.790.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.721
r_dihedral_angle_4_deg18.131
r_dihedral_angle_3_deg12.964
r_dihedral_angle_1_deg6.664
r_scangle_it4.958
r_scbond_it3.041
r_mcangle_it2.064
r_angle_refined_deg1.708
r_mcbond_it1.181
r_angle_other_deg0.976
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.721
r_dihedral_angle_4_deg18.131
r_dihedral_angle_3_deg12.964
r_dihedral_angle_1_deg6.664
r_scangle_it4.958
r_scbond_it3.041
r_mcangle_it2.064
r_angle_refined_deg1.708
r_mcbond_it1.181
r_angle_other_deg0.976
r_mcbond_other0.351
r_chiral_restr0.104
r_bond_refined_d0.02
r_gen_planes_refined0.008
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 Atoms157
Heterogen Atoms28

Software

Software
Software NamePurpose
GDAdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling