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Yeast 20S proteasome soaked with MA9 fraction E/F
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LTC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 MES 100 mM pH 5.5-6.9, MPD 8-18% and magnesium acetate 20 mM
Crystal Properties Matthews coefficient Solvent content 3.69 66.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.892 α = 90 b = 299.287 β = 112.778 c = 144.209 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 PILATUS 2M 2017-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.458 LNLS W01B-MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 3.44 48.8 97.6 0.178 0.216 0.12 0.966 6.4 3 135777
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.44 3.5 92 0.544 0.67 0.384 0.792 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.44 45.74 1.34 135580 6587 97.4 0.203 0.2005 0.2006 0.2517 0.2513 75.72
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.2395 f_angle_d 0.4903 f_chiral_restr 0.0426 f_plane_restr 0.0037 f_bond_d 0.0019
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 49531 Nucleic Acid Atoms Solvent Atoms 332 Heterogen Atoms 411
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction DIMPLE phasing