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Structure of yeast 20S proteasome with Compound 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F16 PDB ENTRY 2F16
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 100 mM MES, 40 mM MgOAc, 15% 2-methyl-2,4-pentanediol (MPD), 10 mM EDTA, pH 7.0, vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.84 67.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.561 α = 90 b = 300.791 β = 112.73 c = 144.707 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 0.97931 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 3.11 150.76 94.1 0.116 7.1 4.1 177491
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) 3.11 3.25 61.2 0.305 2.7
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 2F16 3.11 50 173803 3565 93.93 0.20432 0.20339 0.1998 0.25004 0.2434 RANDOM 65.361
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] 2.88 -1.74 -6.5 2.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.177 r_dihedral_angle_3_deg 18.663 r_dihedral_angle_4_deg 17.793 r_dihedral_angle_1_deg 5.835 r_scangle_it 1.532 r_angle_refined_deg 1.149 r_scbond_it 0.837 r_mcangle_it 0.782 r_mcbond_it 0.413 r_chiral_restr 0.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.177 r_dihedral_angle_3_deg 18.663 r_dihedral_angle_4_deg 17.793 r_dihedral_angle_1_deg 5.835 r_scangle_it 1.532 r_angle_refined_deg 1.149 r_scbond_it 0.837 r_mcangle_it 0.782 r_mcbond_it 0.413 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 49548 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 124
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction