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Structure of yeast 20S open-gate proteasome with Compound 24
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 100 mM MES, pH 7.0, 40 mM MgOAc, 15% 2-methyl-2,4-pentanediol (MPD), 10 mM EDTA, vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.88 68.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.774 α = 90 b = 299.668 β = 113.22 c = 145.301 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 CCD MAR CCD 165 mm M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID APS 31-ID
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 2.6 50 98.7 0.099 9.7 3.7 324018
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 2.6 2.7 87.5 0.397 2.9 28675
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 2.6 50 313121 6321 95.33 0.2098 0.209 0.2047 0.2487 0.2408 RANDOM 54.6343
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] 2.74 -0.62 -4.66 1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.677 r_dihedral_angle_3_deg 17.323 r_dihedral_angle_4_deg 15.896 r_dihedral_angle_1_deg 5.799 r_mcangle_it 1.804 r_angle_refined_deg 1.161 r_mcbond_it 1.05 r_scangle_it 0.89 r_scbond_it 0.549 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.677 r_dihedral_angle_3_deg 17.323 r_dihedral_angle_4_deg 15.896 r_dihedral_angle_1_deg 5.799 r_mcangle_it 1.804 r_angle_refined_deg 1.161 r_mcbond_it 1.05 r_scangle_it 0.89 r_scbond_it 0.549 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 49232 Nucleic Acid Atoms Solvent Atoms 997 Heterogen Atoms 111
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction