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Yeast 20S proteasome in complex with a linear oxindole epoxyketone (compound 6)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CZ4 Yeast 20S proteasome at 2.3 A resolution
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 3.72 66.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.1 α = 90 b = 300.68 β = 113.19 c = 144.7 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 2020-02-16 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 2.8 30 96.1 0.067 14.1 3.1 251692
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 2.8 2.9 98.3 0.58 2.5
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 (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 2.8 30 238960 12577 96.2 0.1841 0.1823 0.1895 0.2184 0.2208 RANDOM 71.341
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] -0.2 -0.6 -1.35 1.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.498 r_dihedral_angle_3_deg 15.001 r_dihedral_angle_4_deg 14.995 r_dihedral_angle_1_deg 6.284 r_long_range_B_refined 4.957 r_long_range_B_other 4.948 r_mcangle_it 3.534 r_mcangle_other 3.533 r_scangle_other 3.402 r_mcbond_it 2.369
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.498 r_dihedral_angle_3_deg 15.001 r_dihedral_angle_4_deg 14.995 r_dihedral_angle_1_deg 6.284 r_long_range_B_refined 4.957 r_long_range_B_other 4.948 r_mcangle_it 3.534 r_mcangle_other 3.533 r_scangle_other 3.402 r_mcbond_it 2.369 r_mcbond_other 2.369 r_scbond_it 2.325 r_scbond_other 2.324 r_angle_refined_deg 1.218 r_angle_other_deg 1.154 r_rigid_bond_restr 0.496 r_chiral_restr 0.04 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 49628 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing