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Yeast 20S proteasome with human beta2c (S171G) in complex with ONX 0914
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 = 135.63 α = 90 b = 300.76 β = 112.88 c = 144.64 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 2016-12-10 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 50 98 0.096 8.4 3.1 256275
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 98.5 0.522 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 2.8 15 241898 12731 97.51 0.1817 0.1798 0.1851 0.21817 0.2221 RANDOM 72.39
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] 0.33 -1.11 -1.64 1.65
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 36.996 r_dihedral_angle_2_deg 34.667 r_sphericity_bonded 29.273 r_dihedral_angle_3_deg 15.033 r_dihedral_angle_4_deg 14.841 r_dihedral_angle_1_deg 5.905 r_long_range_B_refined 5.811 r_long_range_B_other 5.766 r_mcangle_it 5.113 r_mcangle_other 5.113
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 36.996 r_dihedral_angle_2_deg 34.667 r_sphericity_bonded 29.273 r_dihedral_angle_3_deg 15.033 r_dihedral_angle_4_deg 14.841 r_dihedral_angle_1_deg 5.905 r_long_range_B_refined 5.811 r_long_range_B_other 5.766 r_mcangle_it 5.113 r_mcangle_other 5.113 r_scangle_other 4.533 r_mcbond_it 3.78 r_mcbond_other 3.78 r_scbond_it 3.588 r_scbond_other 3.588 r_rigid_bond_restr 1.888 r_angle_refined_deg 1.213 r_angle_other_deg 0.98 r_chiral_restr 0.072 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 48944 Nucleic Acid Atoms Solvent Atoms 429 Heterogen Atoms 322
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC phasing REFMAC refinement