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Yeast 20S proteasome in complex with a linear biarylether epoxyketone (compound 15a)
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 3.68 66.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.21 α = 90 b = 303.14 β = 113.09 c = 143.23 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 2020-05-05 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 3.2 30 97.6 0.091 10.2 3.1 169944
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 3.2 3.3 0.568 2.2
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 3.2 30 161289 8489 97.61 0.18639 0.18421 0.1887 0.2277 0.2277 RANDOM 83.355
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] 3.02 -2.94 -3.03 1.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.215 r_dihedral_angle_4_deg 15.364 r_dihedral_angle_3_deg 14.827 r_dihedral_angle_1_deg 6.172 r_long_range_B_refined 5.662 r_long_range_B_other 5.657 r_mcangle_it 4.046 r_mcangle_other 4.046 r_scangle_other 3.643 r_mcbond_it 2.703
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.215 r_dihedral_angle_4_deg 15.364 r_dihedral_angle_3_deg 14.827 r_dihedral_angle_1_deg 6.172 r_long_range_B_refined 5.662 r_long_range_B_other 5.657 r_mcangle_it 4.046 r_mcangle_other 4.046 r_scangle_other 3.643 r_mcbond_it 2.703 r_mcbond_other 2.703 r_scbond_it 2.419 r_scbond_other 2.418 r_angle_refined_deg 1.193 r_angle_other_deg 1.116 r_rigid_bond_restr 0.376 r_chiral_restr 0.036 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 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 49432 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing