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ADP-ribosylserine hydrolase ARH3 of Latimeria chalumnae in complex with ADP-HPM
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 2.41 48.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.869 α = 90 b = 98.178 β = 90 c = 105.554 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 1.95 44.5 99.8 0.105 0.119 0.057 0.995 8.3 8.5 51249
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 1.95 2 99.3 1.837 2.087 0.977 0.814 0.9 8.6
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 1.95 41.46 48647 2508 99.59 0.18731 0.18587 0.1936 0.2144 0.2177 RANDOM 59.438
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] -1.09 -0.18 1.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.648 r_dihedral_angle_4_deg 19.37 r_dihedral_angle_1_deg 17.468 r_dihedral_angle_3_deg 15.242 r_long_range_B_refined 6.588 r_long_range_B_other 6.545 r_scangle_other 2.041 r_mcangle_it 1.922 r_mcangle_other 1.921 r_scbond_it 1.545
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.648 r_dihedral_angle_4_deg 19.37 r_dihedral_angle_1_deg 17.468 r_dihedral_angle_3_deg 15.242 r_long_range_B_refined 6.588 r_long_range_B_other 6.545 r_scangle_other 2.041 r_mcangle_it 1.922 r_mcangle_other 1.921 r_scbond_it 1.545 r_scbond_other 1.544 r_angle_refined_deg 1.456 r_mcbond_it 1.179 r_mcbond_other 1.177 r_angle_other_deg 1.016 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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 5043 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction DIALS data scaling PHASER phasing