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Crystal Structure of Human UBCH5B C85E
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z6O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 293 10% PEG 200, 0.1 M Bis-Tris propane, pH 9, 15% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.22 44.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.916 α = 90 b = 49.401 β = 90 c = 63.228 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 298 PIXEL DECTRIS EIGER2 X 9M 2024-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.87313 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.25 38.93 98.75 0.04743 0.998 12.33 3.7 41718 20.24
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.295 98.59 0.9445 0.586 1.35 3.8
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 MOLECULAR REPLACEMENT FREE R-VALUE 1.25 38.928 41717 2054 98.752 0.189 0.1885 0.2112 0.2537 21.687
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] 0.134 -0.315 0.181
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29 r_dihedral_angle_4_deg 14.236 r_dihedral_angle_3_deg 12.456 r_dihedral_angle_1_deg 6.637 r_lrange_it 5.646 r_lrange_other 5.601 r_scangle_it 4.788 r_scangle_other 4.782 r_scbond_it 3.43 r_scbond_other 3.416
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29 r_dihedral_angle_4_deg 14.236 r_dihedral_angle_3_deg 12.456 r_dihedral_angle_1_deg 6.637 r_lrange_it 5.646 r_lrange_other 5.601 r_scangle_it 4.788 r_scangle_other 4.782 r_scbond_it 3.43 r_scbond_other 3.416 r_mcangle_other 2.424 r_mcangle_it 2.414 r_angle_refined_deg 1.842 r_mcbond_it 1.715 r_mcbond_other 1.693 r_angle_other_deg 1.667 r_nbd_other 0.276 r_nbd_refined 0.221 r_symmetry_nbd_other 0.191 r_symmetry_xyhbond_nbd_refined 0.181 r_nbtor_refined 0.18 r_symmetry_nbd_refined 0.173 r_xyhbond_nbd_refined 0.129 r_chiral_restr 0.1 r_symmetry_nbtor_other 0.088 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_bond_other_d 0.008 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1168 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Coot model building