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Yeast 20S proteasome mutant: beta5_T3M in complex with MG132
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 3.75 67.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.13 α = 90 b = 300.28 β = 113.08 c = 145.7 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 2015-10-24 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 30 97 0.083 11 3.6 255576
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 98.5 0.458 2.3 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.8 15 242797 12779 97.11 0.18768 0.18675 0.1915 0.20546 0.2101 RANDOM 69.587
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] 3.69 -0.04 -5.52 1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.898 r_sphericity_free 32.393 r_dihedral_angle_3_deg 14.21 r_dihedral_angle_4_deg 14.122 r_sphericity_bonded 5.636 r_dihedral_angle_1_deg 4.699 r_long_range_B_refined 3.101 r_long_range_B_other 3.082 r_mcangle_it 2.666 r_mcangle_other 2.666
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.898 r_sphericity_free 32.393 r_dihedral_angle_3_deg 14.21 r_dihedral_angle_4_deg 14.122 r_sphericity_bonded 5.636 r_dihedral_angle_1_deg 4.699 r_long_range_B_refined 3.101 r_long_range_B_other 3.082 r_mcangle_it 2.666 r_mcangle_other 2.666 r_scangle_other 2.453 r_scbond_it 2.111 r_scbond_other 2.111 r_mcbond_it 2.091 r_mcbond_other 2.091 r_rigid_bond_restr 1.645 r_angle_refined_deg 0.881 r_angle_other_deg 0.706 r_chiral_restr 0.049 r_bond_refined_d 0.005 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 49564 Nucleic Acid Atoms Solvent Atoms 283 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing