3BLJ

Crystal structure of human poly(ADP-ribose) polymerase 15, catalytic fragment


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PQFPDB entry 2PQF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529320% PEG 3350, 0.2M Ammonium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.448.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.21α = 90
b = 68.12β = 90
c = 158.28γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDSi mirrors2007-10-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-30.97908MAX III911-3

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
12.22099.20.1380.1869.74.72544625446
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)
12.22.498.70.5680.5873.24.45711

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 2PQF2.219.78241702417012721000.182530.182530.179350.2434RANDOM24.401
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]
-0.370.250.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.244
r_dihedral_angle_4_deg19.074
r_dihedral_angle_3_deg14.508
r_dihedral_angle_1_deg7.036
r_scangle_it5.232
r_scbond_it3.565
r_mcangle_it2.443
r_angle_refined_deg1.541
r_mcbond_it1.343
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.244
r_dihedral_angle_4_deg19.074
r_dihedral_angle_3_deg14.508
r_dihedral_angle_1_deg7.036
r_scangle_it5.232
r_scbond_it3.565
r_mcangle_it2.443
r_angle_refined_deg1.541
r_mcbond_it1.343
r_nbtor_refined0.307
r_nbd_refined0.2
r_symmetry_hbond_refined0.178
r_symmetry_vdw_refined0.177
r_xyhbond_nbd_refined0.158
r_chiral_restr0.1
r_metal_ion_refined0.095
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3158
Nucleic Acid Atoms
Solvent Atoms288
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing