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Yeast 20S proteasome in complex with glidobactin-like natural product HB333
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 = 136.78 α = 90 b = 300.24 β = 113.32 c = 145.74 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 2.9 30 97 0.083 11.74 3.1 231040
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 2.9 3 0.562 2.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5CZ4 2.9 15 217934 11470 96.47 0.1741 0.1721 0.212 0.193 RANDOM 74.29
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] 1.17 -0.02 -3.17 1.47
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 35.761 r_dihedral_angle_2_deg 35.09 r_sphericity_bonded 27.954 r_dihedral_angle_3_deg 14.61 r_dihedral_angle_4_deg 14.363 r_dihedral_angle_1_deg 5.705 r_rigid_bond_restr 1.135 r_angle_refined_deg 1.131 r_angle_other_deg 0.88 r_chiral_restr 0.062
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 35.761 r_dihedral_angle_2_deg 35.09 r_sphericity_bonded 27.954 r_dihedral_angle_3_deg 14.61 r_dihedral_angle_4_deg 14.363 r_dihedral_angle_1_deg 5.705 r_rigid_bond_restr 1.135 r_angle_refined_deg 1.131 r_angle_other_deg 0.88 r_chiral_restr 0.062 r_bond_refined_d 0.007 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 323 Heterogen Atoms 162
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling REFMAC phasing