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Yeast 20S proteasome in complex with glidobactin-like natural product HB334
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 = 135.72 α = 90 b = 301.64 β = 113.08 c = 144.36 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 2015-04-12 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 97.5 0.061 13.36 3.2 255091
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 98.4 0.543 2.62
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 240805 12674 97.05 0.1758 0.1744 0.1819 0.2022 0.2076 RANDOM 80.187
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] 2.55 -0.91 -5.18 2.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.282 r_sphericity_free 31.132 r_dihedral_angle_3_deg 14.529 r_dihedral_angle_4_deg 14.267 r_sphericity_bonded 7.468 r_dihedral_angle_1_deg 5.729 r_angle_refined_deg 1.125 r_angle_other_deg 0.872 r_rigid_bond_restr 0.818 r_chiral_restr 0.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.282 r_sphericity_free 31.132 r_dihedral_angle_3_deg 14.529 r_dihedral_angle_4_deg 14.267 r_sphericity_bonded 7.468 r_dihedral_angle_1_deg 5.729 r_angle_refined_deg 1.125 r_angle_other_deg 0.872 r_rigid_bond_restr 0.818 r_chiral_restr 0.064 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 366 Heterogen Atoms 154
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling REFMAC phasing