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Yeast 20S proteasome in complex with glidobactin-like natural product HB335
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 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 = 136.16 α = 90 b = 300.12 β = 113.11 c = 144.83 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 PILATUS 6M 2016-11-20 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 99 0.095 10.87 3.1 210818
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 99.7 0.52 2.4
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 15 198714 10458 98.36 0.1682 0.1665 0.173 0.2001 0.2036 RANDOM 66.098
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] 1.77 -0.91 -4.11 2.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.979 r_sphericity_free 29.849 r_sphericity_bonded 21.823 r_dihedral_angle_3_deg 14.612 r_dihedral_angle_4_deg 14.227 r_dihedral_angle_1_deg 5.711 r_rigid_bond_restr 1.164 r_angle_refined_deg 1.119 r_angle_other_deg 0.869 r_chiral_restr 0.061
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.979 r_sphericity_free 29.849 r_sphericity_bonded 21.823 r_dihedral_angle_3_deg 14.612 r_dihedral_angle_4_deg 14.227 r_dihedral_angle_1_deg 5.711 r_rigid_bond_restr 1.164 r_angle_refined_deg 1.119 r_angle_other_deg 0.869 r_chiral_restr 0.061 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 49333 Nucleic Acid Atoms Solvent Atoms 326 Heterogen Atoms 146
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling REFMAC phasing