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RCR E3 ligase E2-Ubiquitin transthiolation intermediate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5O6C 5O6C, 5EGG, 1UBQ experimental model PDB 5EGG 5O6C, 5EGG, 1UBQ experimental model PDB 1UBQ 5O6C, 5EGG, 1UBQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 292 0.85 M sodium citrate, 100 mM sodium chloride, 100 mM Tris-HCl pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.46 50.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 179.008 α = 90 b = 179.008 β = 90 c = 87.276 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 2018-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.2737 ESRF ID29
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 2.58 48.69 98.4 0.103 0.106 0.025 0.999 20.7 17.6 16676
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.58 2.69 91.4 0.434 0.9 9.1
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 5O6C, 5EGG, 1UBQ 2.58 48.69 15778 895 98.34 0.1983 0.1951 0.2018 0.2561 0.2648 RANDOM 78.285
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] -2.62 -1.31 -2.62 8.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.456 r_dihedral_angle_4_deg 19.62 r_dihedral_angle_3_deg 19.106 r_dihedral_angle_1_deg 7.796 r_angle_refined_deg 1.514 r_chiral_restr 0.106 r_bond_refined_d 0.007 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3657 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PDB_EXTRACT data extraction PHASER phasing