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Yeast 20S proteasome with human beta2c (S171G) in complex with 39
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 = 134.14 α = 90 b = 299.85 β = 112.68 c = 143.47 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 2016-11-20 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 3.1 50 98.6 0.098 12.2 3.1 186168
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 3.1 3.2 99.3 0.582 2.6
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 3.1 15 175330 9228 97.85 0.17053 0.1683 0.1766 0.21326 0.2171 RANDOM 77.739
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] 0.48 -1.36 -1.74 1.78
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 44.323 r_dihedral_angle_2_deg 35.152 r_sphericity_bonded 31.972 r_dihedral_angle_3_deg 14.973 r_dihedral_angle_4_deg 14.466 r_long_range_B_refined 6.471 r_long_range_B_other 6.462 r_dihedral_angle_1_deg 6.072 r_mcangle_it 5.681 r_mcangle_other 5.681
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 44.323 r_dihedral_angle_2_deg 35.152 r_sphericity_bonded 31.972 r_dihedral_angle_3_deg 14.973 r_dihedral_angle_4_deg 14.466 r_long_range_B_refined 6.471 r_long_range_B_other 6.462 r_dihedral_angle_1_deg 6.072 r_mcangle_it 5.681 r_mcangle_other 5.681 r_scangle_other 4.964 r_mcbond_it 4.139 r_mcbond_other 4.139 r_scbond_it 3.879 r_scbond_other 3.879 r_angle_refined_deg 1.204 r_angle_other_deg 0.999 r_rigid_bond_restr 0.84 r_chiral_restr 0.072 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 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 48944 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 264
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC phasing REFMAC refinement