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Yeast 20S proteasome soaked with MA9 fraction EF2
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 = 135.374 α = 90 b = 299.672 β = 112.894 c = 144.659 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 3.43 49.56 99.3 0.313 0.339 0.131 0.972 6.4 6.6 139213
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 98.6 1.269 1.374 0.524 0.8 6.7
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 48.9 1.34 138905 6748 99.07 0.1842 0.1816 0.182 0.2351 0.2358 85.16
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 10.8214 f_angle_d 0.534 f_chiral_restr 0.0435 f_plane_restr 0.0039 f_bond_d 0.0021
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 49539 Nucleic Acid Atoms Solvent Atoms 319 Heterogen Atoms 589
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction DIMPLE phasing