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Yeast 20S proteasome with human beta5i (1-138; R57T)
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 = 135.14 α = 90 b = 301.15 β = 112.57 c = 145.06 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 2014-06-07 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 2.4 30 99.1 0.054 14 3.4 411975
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 2.4 2.5 99.2 0.432 3.1
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 2.4 15 391376 20599 99.16 0.20083 0.19987 0.2041 0.21898 0.2232 RANDOM 55.021
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] 2.71 -1.1 -3.84 1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.561 r_sphericity_free 32.018 r_dihedral_angle_3_deg 14.427 r_dihedral_angle_4_deg 13.713 r_sphericity_bonded 12.773 r_dihedral_angle_1_deg 5.141 r_long_range_B_refined 2.784 r_long_range_B_other 2.65 r_mcangle_it 2.063 r_mcangle_other 2.063
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.561 r_sphericity_free 32.018 r_dihedral_angle_3_deg 14.427 r_dihedral_angle_4_deg 13.713 r_sphericity_bonded 12.773 r_dihedral_angle_1_deg 5.141 r_long_range_B_refined 2.784 r_long_range_B_other 2.65 r_mcangle_it 2.063 r_mcangle_other 2.063 r_scangle_other 1.816 r_mcbond_it 1.608 r_mcbond_other 1.608 r_scbond_it 1.575 r_scbond_other 1.575 r_angle_refined_deg 0.866 r_angle_other_deg 0.699 r_rigid_bond_restr 0.696 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 49360 Nucleic Acid Atoms Solvent Atoms 1463 Heterogen Atoms 12
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC phasing REFMAC refinement