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Yeast 20S proteasome in complex with epoxyketone inhibitor 14
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CZ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 292 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 = 135.44 α = 90 b = 300.22 β = 112.98 c = 144.34 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 2015-04-25 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 96.7 0.06 14.8 3.1 280131
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 98.4 0.538 2.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5CZ4 2.7 15 266124 14007 96.79 0.18697 0.18575 0.21004 0.1989 RANDOM 65.465
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] 2.41 -1.31 -5.72 2.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.061 r_sphericity_free 32.826 r_sphericity_bonded 17.583 r_dihedral_angle_4_deg 14.702 r_dihedral_angle_3_deg 14.217 r_dihedral_angle_1_deg 4.995 r_long_range_B_refined 3.718 r_long_range_B_other 3.688 r_mcangle_it 3.288 r_mcangle_other 3.288
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.061 r_sphericity_free 32.826 r_sphericity_bonded 17.583 r_dihedral_angle_4_deg 14.702 r_dihedral_angle_3_deg 14.217 r_dihedral_angle_1_deg 4.995 r_long_range_B_refined 3.718 r_long_range_B_other 3.688 r_mcangle_it 3.288 r_mcangle_other 3.288 r_scangle_other 2.848 r_mcbond_it 2.457 r_mcbond_other 2.457 r_scbond_it 2.306 r_scbond_other 2.306 r_angle_refined_deg 0.938 r_rigid_bond_restr 0.871 r_angle_other_deg 0.805 r_chiral_restr 0.051 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.002 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 49178 Nucleic Acid Atoms Solvent Atoms 450 Heterogen Atoms 216
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC phasing REFMAC refinement