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Yeast 20S proteasome beta5-K33A mutant (propeptide expressed in trans) in complex with Carfilzomib
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 = 136.35 α = 90 b = 300.77 β = 113.16 c = 145.01 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 2.7 30 98.4 0.072 12 3.8 288442
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 98.2 0.474 2.9
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 274019 14423 98.49 0.18815 0.18689 0.191 0.21197 0.2145 RANDOM 66.139
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] 3.38 -1.47 -5.22 1.81
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 36.034 r_dihedral_angle_2_deg 34.111 r_sphericity_bonded 16.439 r_dihedral_angle_3_deg 14.308 r_dihedral_angle_4_deg 13.779 r_dihedral_angle_1_deg 4.86 r_long_range_B_refined 3.898 r_long_range_B_other 3.89 r_mcangle_it 3.441 r_mcangle_other 3.441
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 36.034 r_dihedral_angle_2_deg 34.111 r_sphericity_bonded 16.439 r_dihedral_angle_3_deg 14.308 r_dihedral_angle_4_deg 13.779 r_dihedral_angle_1_deg 4.86 r_long_range_B_refined 3.898 r_long_range_B_other 3.89 r_mcangle_it 3.441 r_mcangle_other 3.441 r_scangle_other 3.043 r_mcbond_it 2.587 r_mcbond_other 2.587 r_scbond_it 2.463 r_scbond_other 2.463 r_rigid_bond_restr 1.033 r_angle_refined_deg 0.899 r_angle_other_deg 0.771 r_chiral_restr 0.049 r_bond_refined_d 0.005 r_bond_other_d 0.003 r_gen_planes_refined 0.003 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 49295 Nucleic Acid Atoms Solvent Atoms 314 Heterogen Atoms 319
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC phasing REFMAC refinement