☰ Navigation Tabs
Human ADP-ribosylserine hydrolase ARH3 mutant E41A in complex with H2B-S7-mar peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6D36
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 sodium citrate (pH 6.1), 18% (w/v) PEG4000 and 400 mM ammonium acetate
Crystal Properties Matthews coefficient Solvent content 2.51 50.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.36 α = 90 b = 158.638 β = 90 c = 74.92 γ = 90
Symmetry Space Group P 21 21 2
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 2019-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.968630 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 1.86 158.62 99.9 0.167 0.171 0.036 0.999 12.9 21.4 124986
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 1.86 1.9 97.7 1.824 1.905 0.532 0.542 1.4 11.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6D36 1.86 97.572 124986 6145 99.205 0.17 0.1685 0.178 0.1946 0.1985 29.039
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] 1.194 0.37 -1.564
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.599 r_dihedral_angle_4_deg 19.571 r_dihedral_angle_3_deg 13.323 r_lrange_it 6.059 r_lrange_other 6.054 r_dihedral_angle_1_deg 5.639 r_scangle_it 3.692 r_scangle_other 3.692 r_mcangle_it 2.662 r_mcangle_other 2.662
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.599 r_dihedral_angle_4_deg 19.571 r_dihedral_angle_3_deg 13.323 r_lrange_it 6.059 r_lrange_other 6.054 r_dihedral_angle_1_deg 5.639 r_scangle_it 3.692 r_scangle_other 3.692 r_mcangle_it 2.662 r_mcangle_other 2.662 r_scbond_it 2.288 r_scbond_other 2.288 r_mcbond_it 1.687 r_mcbond_other 1.683 r_angle_refined_deg 1.56 r_angle_other_deg 1.464 r_symmetry_nbd_refined 0.268 r_nbd_other 0.227 r_nbd_refined 0.226 r_symmetry_nbd_other 0.18 r_xyhbond_nbd_refined 0.17 r_nbtor_refined 0.166 r_symmetry_xyhbond_nbd_refined 0.109 r_symmetry_xyhbond_nbd_other 0.102 r_ncsr_local_group_6 0.094 r_ncsr_local_group_1 0.093 r_ncsr_local_group_5 0.091 r_ncsr_local_group_2 0.089 r_chiral_restr 0.086 r_symmetry_nbtor_other 0.086 r_ncsr_local_group_4 0.074 r_ncsr_local_group_3 0.067 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10274 Nucleic Acid Atoms Solvent Atoms 758 Heterogen Atoms 377
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHENIX phasing