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Yeast 20S proteasome in complex with the vinyl sulfone LU112
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RYP PDB ENTRY 1RYP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 293 20 mM magnesium acetate, 0.1 M MES, 12% MPD, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.7 66.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.91 α = 90 b = 300.9 β = 112.53 c = 143.62 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-F 2011-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0 SLS X06DA
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 3.1 15 92.2 0.063 16.52 3.1 191054 176097 2 2
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 3.1 3.2 94.9 0.469 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1RYP 3.1 15 167291 167291 8805 92.3 0.23 0.21895 0.21795 0.2256 0.23822 0.2475 RANDOM 90.312
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] 5.51 -3.34 -11.17 3.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.005 r_dihedral_angle_3_deg 13.363 r_dihedral_angle_4_deg 9.746 r_dihedral_angle_1_deg 3.892 r_angle_refined_deg 0.806 r_chiral_restr 0.05 r_bond_refined_d 0.004 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 49538 Nucleic Acid Atoms Solvent Atoms 1336 Heterogen Atoms 204
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing