3SMJ

Human poly(ADP-ribose) polymerase 14 (Parp14/Artd8) - catalytic domain in complex with a pyrimidine-like inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3SMIPDB ENTRY 3SMI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529320% PEG 3350, 0.1M Bis-tris, 0.2M Na2SO4, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1943.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.473α = 90
b = 67.755β = 90
c = 144.803γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2010-09-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97908ESRFID29

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
11.53599.10.070.05517.66.46273962739
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)
11.51.5497.30.390.2675.86.44516

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 3SMI1.534.66596025960231371000.182080.182080.18050.21232RANDOM14.533
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]
1.02-1.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.322
r_dihedral_angle_4_deg20.288
r_dihedral_angle_3_deg11.566
r_dihedral_angle_1_deg6.373
r_scangle_it4.477
r_scbond_it2.846
r_mcangle_it1.976
r_angle_refined_deg1.735
r_mcbond_it1.112
r_angle_other_deg0.938
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.322
r_dihedral_angle_4_deg20.288
r_dihedral_angle_3_deg11.566
r_dihedral_angle_1_deg6.373
r_scangle_it4.477
r_scbond_it2.846
r_mcangle_it1.976
r_angle_refined_deg1.735
r_mcbond_it1.112
r_angle_other_deg0.938
r_mcbond_other0.33
r_chiral_restr0.104
r_bond_refined_d0.018
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 Atoms3014
Nucleic Acid Atoms
Solvent Atoms290
Heterogen Atoms34

Software

Software
Software NamePurpose
MxCuBEdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling