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ADP-ribosylserine hydrolase ARH3 of Latimeria chalumnae in complex with ADP-ribose
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 4.5 293.15 200 MM AMMONIUM ACETATE, 21 % PEG4000, 100 MM CITRATE PH 4.5
Crystal Properties Matthews coefficient Solvent content 2.42 49.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.793 α = 90 b = 97.638 β = 90 c = 106.446 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 1.858 71.953 94.9 0.092 0.097 0.032 0.999 14.5 9 36681
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 1.858 2.008 87.7 1.355 1.447 0.494 0.597 1.4 8.3
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 1.86 71.95 34857 1824 61.74 0.1766 0.17482 0.1835 0.20999 0.2201 RANDOM 31.773
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] 0.11 -0.02 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.317 r_dihedral_angle_4_deg 18.253 r_dihedral_angle_3_deg 16.369 r_dihedral_angle_1_deg 5.609 r_long_range_B_refined 3.597 r_long_range_B_other 3.583 r_scangle_other 2.132 r_mcangle_it 1.773 r_mcangle_other 1.773 r_angle_refined_deg 1.489
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.317 r_dihedral_angle_4_deg 18.253 r_dihedral_angle_3_deg 16.369 r_dihedral_angle_1_deg 5.609 r_long_range_B_refined 3.597 r_long_range_B_other 3.583 r_scangle_other 2.132 r_mcangle_it 1.773 r_mcangle_other 1.773 r_angle_refined_deg 1.489 r_scbond_it 1.363 r_scbond_other 1.358 r_mcbond_it 1.058 r_mcbond_other 1.058 r_angle_other_deg 0.992 r_chiral_restr 0.082 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 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 5034 Nucleic Acid Atoms Solvent Atoms 276 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction STARANISO data scaling PHASER phasing