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Structure of UbcH5b in complex with the U-box domain of the E3 ubiquitin ligase CHIP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TGD wild type experimental model PDB 2OXQ wild type, chains C,D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 0.1 M Magnesium chloride hexahydrate, 0.1 M Potassium chloride, 0.1 M PIPES, 20 % v/v PEG Smear Medium
Crystal Properties Matthews coefficient Solvent content 2.62 53.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.081 α = 90 b = 59.138 β = 90 c = 112.834 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 100 CMOS RDI CMOS_8M 2022-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.000020 ALS 4.2.2
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 2.01 41.44 94.1 0.1597 0.1921 0.105 0.988 3.65 6.3 46470 34.56
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.01 2.08 99.8 0.81 0.407 0.9 6.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.01 41.44 1.33 46470 3520 92.94 0.245 0.2415 0.2412 0.2881 0.2879 47.46
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 15.8908 f_angle_d 1.0449 f_chiral_restr 0.06 f_plane_restr 0.0109 f_bond_d 0.0092
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2330 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms 22
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing