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Yeast 20S proteasome in complex with 18
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 = 138.44 α = 90 b = 299.48 β = 113.25 c = 147.31 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 PILATUS3 2M 2016-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 1.0 ESRF ID30B
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 50 98.3 0.064 13.8 3.1 239026
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 99.6 0.551 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 5CZ4 2.9 15 225482 11868 97.78 0.18201 0.1805 0.187 0.21057 0.2144 RANDOM 87.641
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] 2.37 0.29 -5.3 1.95
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 35.261 r_dihedral_angle_2_deg 34.315 r_dihedral_angle_3_deg 14.338 r_dihedral_angle_4_deg 14.31 r_sphericity_bonded 8.403 r_dihedral_angle_1_deg 5.239 r_long_range_B_refined 4.896 r_long_range_B_other 4.878 r_mcangle_it 4.435 r_mcangle_other 4.435
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 35.261 r_dihedral_angle_2_deg 34.315 r_dihedral_angle_3_deg 14.338 r_dihedral_angle_4_deg 14.31 r_sphericity_bonded 8.403 r_dihedral_angle_1_deg 5.239 r_long_range_B_refined 4.896 r_long_range_B_other 4.878 r_mcangle_it 4.435 r_mcangle_other 4.435 r_scangle_other 3.888 r_mcbond_it 3.297 r_mcbond_other 3.297 r_scbond_it 3.11 r_scbond_other 3.109 r_rigid_bond_restr 1.161 r_angle_refined_deg 1.136 r_angle_other_deg 0.895 r_chiral_restr 0.061 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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 49304 Nucleic Acid Atoms Solvent Atoms 233 Heterogen Atoms 178
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC phasing REFMAC refinement