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Crystal structure of hRpn13 Pru domain in complex with Ubiquitin and XL44
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5V1Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 4.6 277 0.1 M Citric acid pH 4.6 and 20% PEG4000
Crystal Properties Matthews coefficient Solvent content 2.9 57.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.35 α = 90 b = 90.283 β = 113.24 c = 65.027 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 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 1.0 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 2.1 48.4 98.54 0.06884 0.08181 0.04364 0.994 9.01 3.4 32724 37.82
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 2.1 2.175 97.07 0.4141 0.5017 0.278 0.915 2.39 3.1
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.1 45.14 1.91 32627 1661 98.55 0.2215 0.2201 0.2209 0.2466 0.2461 RANDOM 45.99
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 15.2292 f_angle_d 1.8307 f_chiral_restr 0.1238 f_bond_d 0.0265 f_plane_restr 0.015
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3018 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms 58
Software Software Software Name Purpose SERGUI data collection DIALS data reduction Aimless data scaling MOLREP phasing Coot model building PHENIX refinement