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Crystal Structure of Yeast Ubc13 C87E
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JBB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1 M sodium cacodylate, pH 6.5, 25% PEG 4000
Crystal Properties Matthews coefficient Solvent content 1.96 37.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 25.603 α = 90 b = 127.663 β = 96.21 c = 42.33 γ = 90
Symmetry Space Group P 1 21 1
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 1.45 42.08 98.06 0.065 0.996 11.87 2.8 46789 16.26
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 1.45 1.502 99.69 0.5799 0.737 2.6 2.9
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.45 42.08 46745 2339 98.074 0.193 0.1913 0.1914 0.228 0.2279 17.453
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] 0.128 0.148 -0.103 -0.056
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.148 r_dihedral_angle_4_deg 15.746 r_dihedral_angle_3_deg 14.662 r_dihedral_angle_1_deg 6.402 r_lrange_it 5.475 r_lrange_other 5.341 r_scangle_it 4.077 r_scangle_other 4.076 r_scbond_it 2.772 r_scbond_other 2.771
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.148 r_dihedral_angle_4_deg 15.746 r_dihedral_angle_3_deg 14.662 r_dihedral_angle_1_deg 6.402 r_lrange_it 5.475 r_lrange_other 5.341 r_scangle_it 4.077 r_scangle_other 4.076 r_scbond_it 2.772 r_scbond_other 2.771 r_mcangle_it 2.416 r_mcangle_other 2.415 r_angle_refined_deg 1.758 r_mcbond_it 1.672 r_mcbond_other 1.671 r_angle_other_deg 1.49 r_symmetry_nbd_refined 0.361 r_nbd_other 0.274 r_nbd_refined 0.231 r_symmetry_xyhbond_nbd_refined 0.219 r_symmetry_nbd_other 0.214 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.145 r_chiral_restr 0.092 r_symmetry_nbtor_other 0.088 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2366 Nucleic Acid Atoms Solvent Atoms 292 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Coot model building