6HH6

Human poly(ADP-ribose) glycohydrolase in complex with ADP-HPM


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5A7R 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.1520% PEG3350, 0.2 M AMMONIUM SULFATE, 0.1 M PCTP PH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.550.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.316α = 90
b = 90.875β = 90
c = 95.276γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-02-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9174DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.8554.0999.80.2210.2390.0640.9961013.350546
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.8999.22.6742.9161.150.5971.312.3

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 REPLACEMENTTHROUGHOUT5A7R1.8554.1548074240899.760.167590.165950.20027RANDOM24.94
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]
-1.60.710.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.374
r_dihedral_angle_4_deg19.079
r_dihedral_angle_3_deg14.647
r_dihedral_angle_1_deg6.895
r_long_range_B_refined5.839
r_long_range_B_other5.67
r_scangle_other2.421
r_mcangle_it2.073
r_mcangle_other2.073
r_angle_refined_deg1.578
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.374
r_dihedral_angle_4_deg19.079
r_dihedral_angle_3_deg14.647
r_dihedral_angle_1_deg6.895
r_long_range_B_refined5.839
r_long_range_B_other5.67
r_scangle_other2.421
r_mcangle_it2.073
r_mcangle_other2.073
r_angle_refined_deg1.578
r_scbond_it1.529
r_scbond_other1.488
r_mcbond_it1.241
r_mcbond_other1.24
r_angle_other_deg1.015
r_chiral_restr0.089
r_bond_refined_d0.012
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4098
Nucleic Acid Atoms
Solvent Atoms505
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
xia2data scaling
PHASERphasing