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Yeast 20S proteasome beta5-T1A mutant in complex with Syringolin A, propeptide expressed in trans
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, 0.1 M MES
Crystal Properties Matthews coefficient Solvent content 3.67 66.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.04 α = 90 b = 301.44 β = 113.27 c = 145.75 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 2012-12-08 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 2.7 30 97.4 0.078 9.8 2.9 292182 284585
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 2.7 2.8 99.4 0.513 2.2
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 15 270355 14230 97.51 0.19601 0.19443 0.198 0.22606 0.2281 RANDOM 63.252
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] 4.27 -0.51 -6.16 1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.503 r_sphericity_free 29.654 r_sphericity_bonded 17.295 r_dihedral_angle_4_deg 14.469 r_dihedral_angle_3_deg 14.46 r_dihedral_angle_1_deg 5.157 r_long_range_B_refined 3.888 r_long_range_B_other 3.851 r_mcangle_it 3.334 r_mcangle_other 3.333
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.503 r_sphericity_free 29.654 r_sphericity_bonded 17.295 r_dihedral_angle_4_deg 14.469 r_dihedral_angle_3_deg 14.46 r_dihedral_angle_1_deg 5.157 r_long_range_B_refined 3.888 r_long_range_B_other 3.851 r_mcangle_it 3.334 r_mcangle_other 3.333 r_scangle_other 3.084 r_mcbond_it 2.485 r_mcbond_other 2.485 r_scbond_it 2.465 r_scbond_other 2.464 r_rigid_bond_restr 1.164 r_angle_refined_deg 0.859 r_angle_other_deg 0.688 r_chiral_restr 0.05 r_bond_refined_d 0.004 r_gen_planes_refined 0.002 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 49372 Nucleic Acid Atoms Solvent Atoms 448 Heterogen Atoms 81
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC phasing REFMAC refinement