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Yeast 20S proteasome with human beta5i (1-138; V31M) and human beta6 (97-111; 118-133) in complex with epoxyketone inhibitor 16
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 6.8 293 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 = 135.75 α = 90 b = 300.02 β = 113.05 c = 145.64 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 DECTRIS EIGER X 16M 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 2.9 30 98.5 0.079 14.8 4 232923
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 2.9 3 99.3 0.547 3.5
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 5CZ4 2.9 15 221276 11647 98.67 0.17239 0.17117 0.1772 0.19533 0.2 RANDOM 64.918
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] 3.33 -0.76 -4.72 1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.016 r_sphericity_free 33.62 r_dihedral_angle_3_deg 14.306 r_dihedral_angle_4_deg 14.16 r_sphericity_bonded 12.582 r_dihedral_angle_1_deg 4.826 r_long_range_B_refined 3.758 r_long_range_B_other 3.75 r_mcangle_it 3.264 r_mcangle_other 3.264
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.016 r_sphericity_free 33.62 r_dihedral_angle_3_deg 14.306 r_dihedral_angle_4_deg 14.16 r_sphericity_bonded 12.582 r_dihedral_angle_1_deg 4.826 r_long_range_B_refined 3.758 r_long_range_B_other 3.75 r_mcangle_it 3.264 r_mcangle_other 3.264 r_scangle_other 3.089 r_scbond_it 2.532 r_scbond_other 2.532 r_mcbond_it 2.449 r_mcbond_other 2.449 r_rigid_bond_restr 0.968 r_angle_refined_deg 0.875 r_angle_other_deg 0.707 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 49384 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing