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Yeast 20S proteasome beta5-K33A mutant (propeptide expressed in trans) in complex with MG132
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 = 136.92 α = 90 b = 299.86 β = 113.13 c = 145.98 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 2015-12-10 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 2.8 40 97.3 0.079 11.7 3.9 257992
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 2.8 2.9 98 0.486 3
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 2.8 15 245092 12900 97.4 0.18 0.178 0.1822 0.206 0.21 RANDOM 70.64
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] 3.08 -0.63 -5.3 1.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.933 r_sphericity_free 30.79 r_sphericity_bonded 16.7 r_dihedral_angle_3_deg 14.136 r_dihedral_angle_4_deg 14.036 r_dihedral_angle_1_deg 4.834 r_long_range_B_refined 4.701 r_long_range_B_other 4.686 r_mcangle_it 4.049 r_mcangle_other 4.049
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.933 r_sphericity_free 30.79 r_sphericity_bonded 16.7 r_dihedral_angle_3_deg 14.136 r_dihedral_angle_4_deg 14.036 r_dihedral_angle_1_deg 4.834 r_long_range_B_refined 4.701 r_long_range_B_other 4.686 r_mcangle_it 4.049 r_mcangle_other 4.049 r_scangle_other 3.802 r_mcbond_it 3.034 r_mcbond_other 3.034 r_scbond_it 3.028 r_scbond_other 3.028 r_rigid_bond_restr 1.306 r_angle_refined_deg 0.855 r_angle_other_deg 0.682 r_chiral_restr 0.049 r_bond_refined_d 0.004 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 49358 Nucleic Acid Atoms Solvent Atoms 259 Heterogen Atoms 216
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing