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Yeast 20S proteasome in complex with the covalently bound inhibitor b-lactone (2R,3S)-3-isopropyl-4-oxo-2-oxetane-carboxylate (IOC)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CZ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 293 20 mM MgAC2, 13% MPD, 0.1 M MES
Crystal Properties Matthews coefficient Solvent content 3.67 66.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.12 α = 90 b = 301.5 β = 112.93 c = 144.25 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 PSI JUNGFRAU 16M 2021-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3 30 96.2 0.085 9.1 3.1 203690
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.1 0.577 2
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 5CZ4 3 30 193349 10176 96.26 0.1798 0.1779 0.1819 0.2158 0.2168 RANDOM 90.54
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] 3.58 -2.11 -3.1 0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.109 r_dihedral_angle_3_deg 14.673 r_dihedral_angle_4_deg 13.545 r_dihedral_angle_1_deg 5.997 r_angle_refined_deg 1.188 r_angle_other_deg 1.154 r_rigid_bond_restr 0.331 r_chiral_restr 0.035 r_bond_refined_d 0.002 r_gen_planes_refined 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.109 r_dihedral_angle_3_deg 14.673 r_dihedral_angle_4_deg 13.545 r_dihedral_angle_1_deg 5.997 r_angle_refined_deg 1.188 r_angle_other_deg 1.154 r_rigid_bond_restr 0.331 r_chiral_restr 0.035 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 49300 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling REFMAC phasing