4B1J

Structure of human PARG catalytic domain in complex with ADP-HPD


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
125% PEG 3350, 36.4 MM PCTP-4, 63.6 MM PCTP-10, 0.2 M AMMONIUM SULPHATE
Crystal Properties
Matthews coefficientSolvent content
2.4750.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.848α = 90
b = 90.971β = 90
c = 94.763γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944VARIMAXHF2010-03-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E

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
12.0894.7690.20.1112.46.3321762
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)
12.082.1952.70.492.83.7

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 4A0D2.0865.6330387160190.370.170180.16780.21475RANDOM24.065
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]
-2.01-0.232.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.158
r_dihedral_angle_4_deg15.777
r_dihedral_angle_3_deg15.122
r_dihedral_angle_1_deg6.087
r_scangle_it3.033
r_scbond_it1.915
r_angle_refined_deg1.416
r_mcangle_it1.298
r_angle_other_deg1.103
r_mcbond_it0.718
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.158
r_dihedral_angle_4_deg15.777
r_dihedral_angle_3_deg15.122
r_dihedral_angle_1_deg6.087
r_scangle_it3.033
r_scbond_it1.915
r_angle_refined_deg1.416
r_mcangle_it1.298
r_angle_other_deg1.103
r_mcbond_it0.718
r_mcbond_other0.164
r_chiral_restr0.09
r_bond_refined_d0.014
r_bond_other_d0.006
r_gen_planes_refined0.006
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_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 Atoms4060
Nucleic Acid Atoms
Solvent Atoms529
Heterogen Atoms62

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
AMoREphasing