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Catalytic domain of the human ubiquitin-conjugating enzyme UBE2S C118M
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZDN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.2 M magnesium chloride, 0.1 M hepes pH 7.5, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.61 52.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.619 α = 90 b = 84.619 β = 90 c = 87.832 γ = 120
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 PILATUS 6M-F 2016-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9762 PETRA III, EMBL c/o DESY P14 (MX2)
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 2.9 42.309 99.94 0.02634 0.03725 0.02634 0.999 21.4 2 7984 63.58
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 2.9 3.004 100 0.1729 0.2445 0.1729 0.896 4.19 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1ZDN 2.9 42.309 1.38 7984 439 99.97 0.187 0.1843 0.23 0.217
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.894 f_angle_d 0.704 f_chiral_restr 0.044 f_plane_restr 0.005 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2254 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 16
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing