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Yeast 20S proteasome in complex with an engineered fellutamide derivative (C14QAL)
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 6.8 293 100 mM MES, 20 mM MgAc2, 11% MPD
Crystal Properties Matthews coefficient Solvent content 3.68 66.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.97 α = 90 b = 300.87 β = 112.78 c = 143.98 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 2021-08-21 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 3.25 30 95.1 0.105 11.1 3 157953
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 3.25 3.35 93.7 0.654 2.4 2.8
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 1RYP 3.25 30 149904 7890 95.15 0.1764 0.1745 0.1882 0.21218 0.2206 RANDOM 91.345
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] 6.51 -3.33 -5.78 1.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.811 r_dihedral_angle_3_deg 14.527 r_dihedral_angle_4_deg 13.74 r_dihedral_angle_1_deg 6.045 r_long_range_B_refined 5.738 r_long_range_B_other 5.737 r_mcangle_it 4.032 r_mcangle_other 4.032 r_scangle_other 3.678 r_mcbond_it 2.676
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.811 r_dihedral_angle_3_deg 14.527 r_dihedral_angle_4_deg 13.74 r_dihedral_angle_1_deg 6.045 r_long_range_B_refined 5.738 r_long_range_B_other 5.737 r_mcangle_it 4.032 r_mcangle_other 4.032 r_scangle_other 3.678 r_mcbond_it 2.676 r_mcbond_other 2.676 r_scbond_it 2.448 r_scbond_other 2.447 r_angle_other_deg 1.205 r_angle_refined_deg 1.204 r_rigid_bond_restr 0.357 r_chiral_restr 0.039 r_bond_refined_d 0.003 r_bond_other_d 0.003 r_gen_planes_refined 0.003 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 49322 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 159
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing