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Yeast 20S proteasome in complex with PR-VI modulator
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RYP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 293 30mM magnesium acetate, 12% MPD, 0.1M MES pH 7.2
Crystal Properties Matthews coefficient Solvent content 3.49 64.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.35 α = 90 b = 300.79 β = 112.11 c = 144.58 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 CCD ADSC QUANTUM 315 2011-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.979 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.7 49.46 68.4 0.192 6.5 1 207816
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.72 20.2 2.9 1
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 1RYP 2.7 49.46 186914 9928 68.32 0.17957 0.17733 0.1813 0.22192 0.2209 RANDOM 44.523
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] 2.19 -1.55 0.42 -1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.984 r_dihedral_angle_4_deg 18.397 r_dihedral_angle_3_deg 18.371 r_dihedral_angle_1_deg 7.167 r_long_range_B_refined 6.019 r_long_range_B_other 6.017 r_scangle_other 3.353 r_mcangle_it 2.565 r_mcangle_other 2.565 r_scbond_it 2.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.984 r_dihedral_angle_4_deg 18.397 r_dihedral_angle_3_deg 18.371 r_dihedral_angle_1_deg 7.167 r_long_range_B_refined 6.019 r_long_range_B_other 6.017 r_scangle_other 3.353 r_mcangle_it 2.565 r_mcangle_other 2.565 r_scbond_it 2.013 r_scbond_other 2.012 r_angle_refined_deg 1.684 r_mcbond_it 1.523 r_mcbond_other 1.523 r_angle_other_deg 0.98 r_chiral_restr 0.084 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.004 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 49481 Nucleic Acid Atoms Solvent Atoms 359 Heterogen Atoms 356
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction Coot model building MOLREP phasing HKL-3000 data scaling