6G2A

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5293.15100 mM magnesium acetate, 12 % (w/v) PEG8000, 100 mM MOPS pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.0439.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.526α = 90
b = 42.94β = 118.93
c = 89.231γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-01-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I041.0036DiamondI04

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
11.878.0999.40.070.0830.0440.99912.86.430388
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)
11.81.8499.50.4880.5750.3020.8862.75

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 REPLACEMENTTHROUGHOUT3HFW1.878.0928819156999.390.183510.181430.22039RANDOM30.432
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]
-1.28-1.022.160.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.265
r_dihedral_angle_3_deg15.507
r_dihedral_angle_4_deg15.443
r_dihedral_angle_1_deg6.063
r_long_range_B_refined2.28
r_long_range_B_other2.247
r_angle_refined_deg1.455
r_scangle_other1.257
r_angle_other_deg1.031
r_mcangle_it0.931
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.265
r_dihedral_angle_3_deg15.507
r_dihedral_angle_4_deg15.443
r_dihedral_angle_1_deg6.063
r_long_range_B_refined2.28
r_long_range_B_other2.247
r_angle_refined_deg1.455
r_scangle_other1.257
r_angle_other_deg1.031
r_mcangle_it0.931
r_mcangle_other0.931
r_scbond_it0.8
r_scbond_other0.8
r_mcbond_it0.594
r_mcbond_other0.589
r_chiral_restr0.08
r_bond_refined_d0.011
r_gen_planes_refined0.008
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2814
Nucleic Acid Atoms
Solvent Atoms132
Heterogen Atoms49

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
DIALSdata scaling
PHASERphasing