4NA5 | pdb_00004na5

Crystal structure of mouse poly(ADP-ribose) glycohydrolase (PARG) catalytic domain mutant E748N


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
162770.2M (NH4)2SO4, 16% PEG3,350, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal Properties
Matthews coefficientSolvent content
2.6453.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.091α = 90
b = 91.293β = 90
c = 103.504γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.1ALS8.2.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
125099.3434751.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0692.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2504382643291218998.80.1820.180.180.2140.22RANDOM24.16
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]
-0.190.010.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.042
r_dihedral_angle_3_deg12.173
r_dihedral_angle_4_deg11.814
r_dihedral_angle_1_deg5.952
r_scangle_it4.271
r_scbond_it2.794
r_mcangle_it2.177
r_mcbond_it1.409
r_angle_refined_deg1.138
r_angle_other_deg0.843
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.042
r_dihedral_angle_3_deg12.173
r_dihedral_angle_4_deg11.814
r_dihedral_angle_1_deg5.952
r_scangle_it4.271
r_scbond_it2.794
r_mcangle_it2.177
r_mcbond_it1.409
r_angle_refined_deg1.138
r_angle_other_deg0.843
r_mcbond_other0.44
r_chiral_restr0.07
r_bond_refined_d0.009
r_gen_planes_refined0.005
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_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 Atoms407
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing