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Yeast 20S proteasome soaked with isolated TMC-86A
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 6.9 291 MES 100 mM pH 6.9, MPD 25% and magnesium acetate 20 mM
Crystal Properties Matthews coefficient Solvent content 3.29 62.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.315 α = 90 b = 298.278 β = 108.795 c = 144.573 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 2024-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS SIRIUS BEAMLINE MANACA 0.9772 LNLS SIRIUS MANACA
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 3.04 48.54 99.91 0.327 0.3542 0.1349 0.986 5.48 6.8 240562 58.03
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 3.04 3.07 99.88 3.273 3.545 1.35 0.262 0.61 6.8
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 3.04 48.54 1.34 179710 8947 99.91 0.1767 0.1744 0.1745 0.2205 0.22 60.44
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 13.1167 f_angle_d 0.5918 f_chiral_restr 0.0447 f_plane_restr 0.0043 f_bond_d 0.0027
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 49387 Nucleic Acid Atoms Solvent Atoms 337 Heterogen Atoms 501
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing