6G28

Human [protein ADP-ribosylargenine] hydrolase ARH1 in complex with ADP-ribose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3HFW 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.15200 mM magnesium formate, 20 % (w/v) PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.244.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.102α = 90
b = 66.687β = 90
c = 83.42γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2017-12-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9760DiamondI03

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
11.2366.6999.60.0590.0640.0250.99821.712.2103868
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)
11.231.2597.10.2620.2950.1320.9815.59.3

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 REPLACEMENTTHROUGHOUT3HFW1.2352.0998756503499.570.145660.145060.15744RANDOM19.97
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]
1.02-0.57-0.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.93
r_dihedral_angle_4_deg15.897
r_dihedral_angle_3_deg13.536
r_dihedral_angle_1_deg5.305
r_long_range_B_refined3.083
r_long_range_B_other2.799
r_angle_refined_deg1.527
r_scangle_other1.513
r_angle_other_deg1.118
r_scbond_it0.973
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.93
r_dihedral_angle_4_deg15.897
r_dihedral_angle_3_deg13.536
r_dihedral_angle_1_deg5.305
r_long_range_B_refined3.083
r_long_range_B_other2.799
r_angle_refined_deg1.527
r_scangle_other1.513
r_angle_other_deg1.118
r_scbond_it0.973
r_scbond_other0.971
r_mcangle_other0.914
r_mcangle_it0.911
r_mcbond_it0.573
r_mcbond_other0.564
r_chiral_restr0.089
r_bond_refined_d0.01
r_gen_planes_refined0.007
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 Atoms2794
Nucleic Acid Atoms
Solvent Atoms347
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
DIALSdata scaling
PHASERphasing