5A7R

Human poly(ADP-ribose) glycohydrolase in complex with synthetic dimeric ADP-ribose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4A0DPDB ENTRY 4A0D

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1820% PEG3350, 0.2 M AMMONIUM SULFATE, 0.1 M PCTP PH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.5451

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.457α = 90
b = 91.277β = 90
c = 96.123γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2MTORROIDAL MIRROR2014-08-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-1DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.9555.2299.90.121.413.244881
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.95299.80.584.912.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4A0D1.9566.1941801213199.880.139280.13730.1789RANDOM22.196
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]
-1.49-0.271.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.762
r_dihedral_angle_4_deg17.86
r_dihedral_angle_3_deg13.914
r_dihedral_angle_1_deg6.674
r_scangle_it5.029
r_scbond_it3.355
r_mcangle_it2.944
r_mcbond_it2.001
r_mcbond_other1.991
r_angle_refined_deg1.547
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.762
r_dihedral_angle_4_deg17.86
r_dihedral_angle_3_deg13.914
r_dihedral_angle_1_deg6.674
r_scangle_it5.029
r_scbond_it3.355
r_mcangle_it2.944
r_mcbond_it2.001
r_mcbond_other1.991
r_angle_refined_deg1.547
r_angle_other_deg1.053
r_chiral_restr0.106
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_gen_planes_other0.002
r_bond_other_d0.001
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4097
Nucleic Acid Atoms
Solvent Atoms422
Heterogen Atoms197

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing