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Structure of yeast 20S open-gate proteasome with Compound 20
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G0U PDB entry 1G0U
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 68.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.6 α = 90 b = 299.45 β = 113.17 c = 145.483 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 2.65 30 95.8 0.099 9.5 3.7 297624
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 2.65 2.74 78.8 0.378 2.8 24439
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 PDB entry 1G0U 2.65 30 296915 5996 95.4 0.2193 0.2186 0.2152 0.2532 0.2461 RANDOM 47.8467
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] 2.42 -0.49 -4.43 1.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.134 r_dihedral_angle_4_deg 18.044 r_dihedral_angle_3_deg 17.922 r_dihedral_angle_1_deg 5.921 r_scangle_it 2.58 r_scbond_it 1.44 r_angle_refined_deg 1.258 r_mcangle_it 1.092 r_mcbond_it 0.56 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.134 r_dihedral_angle_4_deg 18.044 r_dihedral_angle_3_deg 17.922 r_dihedral_angle_1_deg 5.921 r_scangle_it 2.58 r_scbond_it 1.44 r_angle_refined_deg 1.258 r_mcangle_it 1.092 r_mcbond_it 0.56 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 48883 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 128
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction