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Ligand-induced Lys33-Thr1 crosslinking at subunit beta5 of the yeast 20S proteasome
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 6.8 293 20 MM MGAC2, 13% MPD, PH 6.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties Matthews coefficient Solvent content 3.67 66.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.58 α = 90 b = 300.82 β = 113.2 c = 146.29 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 PSI PILATUS 6M 2013-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 2.4 30 96.9 0.044 17.3 3.1 408278 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 2.4 2.5 97.8 0.417 4
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 1RYP 2.4 15 408277 387863 20414 96.99 0.181 0.17806 0.17718 0.1814 0.19486 0.1975 RANDOM 56.74
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] 3.41 -0.67 -4.79 1.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.121 r_sphericity_free 25.257 r_dihedral_angle_3_deg 17.178 r_dihedral_angle_4_deg 17.176 r_sphericity_bonded 8.08 r_dihedral_angle_1_deg 5.801 r_long_range_B_refined 2.617 r_long_range_B_other 2.504 r_scangle_other 1.956 r_scbond_it 1.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.121 r_sphericity_free 25.257 r_dihedral_angle_3_deg 17.178 r_dihedral_angle_4_deg 17.176 r_sphericity_bonded 8.08 r_dihedral_angle_1_deg 5.801 r_long_range_B_refined 2.617 r_long_range_B_other 2.504 r_scangle_other 1.956 r_scbond_it 1.93 r_scbond_other 1.929 r_mcangle_it 1.848 r_mcangle_other 1.848 r_mcbond_it 1.576 r_mcbond_other 1.576 r_rigid_bond_restr 1.47 r_angle_refined_deg 0.976 r_angle_other_deg 0.706 r_chiral_restr 0.056 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 49352 Nucleic Acid Atoms Solvent Atoms 1740 Heterogen Atoms 23
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing