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Crystal structure of hRpn13 Pru bound with U-shaped peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IRS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 4.6 277.15 0.1 M sodium acetate pH 4.6 and 22% PEG3350
Crystal Properties Matthews coefficient Solvent content 1.96 37.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.262 α = 90 b = 56.974 β = 90 c = 77.793 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 PIXEL DECTRIS EIGER X 16M 2021-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.979 APS 22-ID
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 1.85 38.9 99.5 0.073 0.08 0.031 0.998 13.9 6.4 12367 17.78
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 1.85 1.89 99.8 0.238 0.258 0.099 0.973 6.7
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 1.85 38.9 1.92 12321 582 99.27 0.1961 0.1952 0.2001 0.216 0.2196 18.28
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 13.2355 f_angle_d 1.3102 f_chiral_restr 0.0819 f_plane_restr 0.0217 f_bond_d 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 968 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms 8
Software Software Software Name Purpose SERGUI data collection DIALS data reduction Coot model building REFMAC refinement