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Ligand-induced aziridine-formation 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 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 = 134.72 α = 90 b = 301.36 β = 112.81 c = 144.74 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 2013-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 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 2.1 30 98.8 0.044 18.3 3.1 608720 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 2.1 2.2 99.4 0.568 2.9
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 (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 2.1 15 608720 578284 30436 98.9 0.186 0.185 0.1912 0.198 0.2033 RANDOM 46.42
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] 1.89 -0.5 -3.72 1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.265 r_sphericity_free 23.417 r_dihedral_angle_4_deg 18.338 r_dihedral_angle_3_deg 17.436 r_dihedral_angle_1_deg 6.174 r_sphericity_bonded 4.251 r_long_range_B_refined 2.366 r_long_range_B_other 2.056 r_rigid_bond_restr 1.892 r_scbond_it 1.771
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.265 r_sphericity_free 23.417 r_dihedral_angle_4_deg 18.338 r_dihedral_angle_3_deg 17.436 r_dihedral_angle_1_deg 6.174 r_sphericity_bonded 4.251 r_long_range_B_refined 2.366 r_long_range_B_other 2.056 r_rigid_bond_restr 1.892 r_scbond_it 1.771 r_scbond_other 1.771 r_scangle_other 1.514 r_mcangle_it 1.289 r_mcangle_other 1.289 r_mcbond_it 1.238 r_mcbond_other 1.238 r_angle_refined_deg 1.095 r_angle_other_deg 0.744 r_chiral_restr 0.096 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 49336 Nucleic Acid Atoms Solvent Atoms 3472 Heterogen Atoms 23
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing