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ADP-ribosylserine hydrolase ARH3 of Latimeria chalumnae in complex with ADP-ribosyl-L-arginine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FOZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293.15 200 MM AMMONIUM ACETATE, 25 % (W/V), PEG4000, 100 MM CITRATE PH 5.6
Crystal Properties Matthews coefficient Solvent content 2.39 48.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.145 α = 90 b = 96.642 β = 90 c = 105.908 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2018-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.66 71.39 100 0.089 0.101 0.047 0.997 9.9 8.3 82067
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) Redundancy Number Unique Reflections (All) 1 1.66 1.7 100 1.524 1.733 0.809 0.676 8.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2FOZ 1.66 71.39 77918 4030 99.81 0.16965 0.16855 0.179 0.18994 0.1972 RANDOM 32.064
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] -1.33 -1.7 3.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.788 r_dihedral_angle_4_deg 18.297 r_dihedral_angle_3_deg 13.074 r_dihedral_angle_1_deg 5.479 r_long_range_B_refined 4.552 r_long_range_B_other 4.481 r_scangle_other 2.597 r_mcangle_it 1.818 r_mcangle_other 1.817 r_scbond_it 1.676
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.788 r_dihedral_angle_4_deg 18.297 r_dihedral_angle_3_deg 13.074 r_dihedral_angle_1_deg 5.479 r_long_range_B_refined 4.552 r_long_range_B_other 4.481 r_scangle_other 2.597 r_mcangle_it 1.818 r_mcangle_other 1.817 r_scbond_it 1.676 r_scbond_other 1.675 r_angle_refined_deg 1.531 r_mcbond_it 1.142 r_mcbond_other 1.14 r_angle_other_deg 1.063 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 5039 Nucleic Acid Atoms Solvent Atoms 521 Heterogen Atoms 118
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction DIALS data scaling PHASER phasing