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Crystal structure of the catalytic domain of human ubiquitin ligase AREL1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.4 289 0.1M Sodium phosphate pH 6.4, 0.2M Potassium chloride, 2.25M Sodium chloride
Crystal Properties Matthews coefficient Solvent content 4.13 70.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.231 α = 90 b = 150.231 β = 90 c = 342.645 γ = 120
Symmetry Space Group P 65 2 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 CCD ADSC QUANTUM 315r 2019-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9792 SSRF BL17U
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 3.207 50 98 0.119 0.141 0.071 0.979 9.6 3.4 38276
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 3.25 3.31 98.9 0.628 0.742 0.381 0.635 2.06 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION SAD FREE R-VALUE 3.207 49.223 38276 1878 99.83 0.211 0.2108 0.2249 0.1982 68.887
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] -0.02 -0.01 -0.02 0.065
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.978 r_dihedral_angle_3_deg 22.813 r_dihedral_angle_4_deg 19.33 r_lrange_it 10.216 r_lrange_other 10.216 r_dihedral_angle_1_deg 7.536 r_scangle_it 6.961 r_scangle_other 6.961 r_mcangle_it 6.912 r_mcangle_other 6.912
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.978 r_dihedral_angle_3_deg 22.813 r_dihedral_angle_4_deg 19.33 r_lrange_it 10.216 r_lrange_other 10.216 r_dihedral_angle_1_deg 7.536 r_scangle_it 6.961 r_scangle_other 6.961 r_mcangle_it 6.912 r_mcangle_other 6.912 r_mcbond_it 4.189 r_mcbond_other 4.181 r_scbond_it 4.123 r_scbond_other 4.123 r_angle_refined_deg 1.625 r_angle_other_deg 1.303 r_symmetry_nbd_refined 0.364 r_symmetry_xyhbond_nbd_refined 0.313 r_nbd_refined 0.231 r_symmetry_nbd_other 0.21 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.178 r_nbd_other 0.16 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.085 r_ext_dist_refined_d 0.084 r_symmetry_xyhbond_nbd_other 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8984 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing