4B1G

Structure of unliganded human PARG catalytic domain


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
128% PEG3350, 0.2M MAGNESIUM CHLORIDE, 0.1M PCTP (0.04M SODIUM PROPIONATE, 0.02M SODIUM CACODYLATE, 0.04M BIS-TRIS PROPANE) PH 7.5; 1:1 RATIO; 4 MICROLITRE DROP; ROOM TEMPERATURE
Crystal Properties
Matthews coefficientSolvent content
2.3647.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.759α = 90
b = 66.387β = 95.26
c = 89.323γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORS2009-11-19MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.979, 0.975, 0.982ESRFID23-1

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
11.8388.9986.30.1112.46.3394972
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)
11.831.9347.90.3822.2

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 DIFFRACTIONMADTHROUGHOUTNONE1.8366.4336906198584.760.184920.183130.21794RANDOM26.243
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]
-0.19-0.520.62-0.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.596
r_dihedral_angle_4_deg17.328
r_dihedral_angle_3_deg15.464
r_dihedral_angle_1_deg5.986
r_scangle_it3.528
r_scbond_it2.42
r_angle_other_deg1.699
r_mcangle_it1.487
r_angle_refined_deg1.444
r_mcbond_it0.826
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.596
r_dihedral_angle_4_deg17.328
r_dihedral_angle_3_deg15.464
r_dihedral_angle_1_deg5.986
r_scangle_it3.528
r_scbond_it2.42
r_angle_other_deg1.699
r_mcangle_it1.487
r_angle_refined_deg1.444
r_mcbond_it0.826
r_mcbond_other0.211
r_chiral_restr0.098
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d0.002
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 Atoms3985
Nucleic Acid Atoms
Solvent Atoms294
Heterogen Atoms13

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
SHELXphasing