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Yeast 20S proteasome with human beta2i (1-53) in complex with 43
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 = 134.24 α = 90 b = 299.9 β = 112.5 c = 143.25 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 50 98.2 0.091 11.8 3.1 204830
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 3.1 99.2 0.592 2.2
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 15 193054 10161 97.58 0.16648 0.16461 0.1746 0.20199 0.208 RANDOM 75.079
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] 2.1 -1.82 -3.11 1.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.408 r_sphericity_free 34.02 r_sphericity_bonded 25.818 r_dihedral_angle_3_deg 14.654 r_dihedral_angle_4_deg 14.146 r_dihedral_angle_1_deg 5.932 r_long_range_B_refined 5.769 r_long_range_B_other 5.76 r_mcangle_it 5.098 r_mcangle_other 5.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.408 r_sphericity_free 34.02 r_sphericity_bonded 25.818 r_dihedral_angle_3_deg 14.654 r_dihedral_angle_4_deg 14.146 r_dihedral_angle_1_deg 5.932 r_long_range_B_refined 5.769 r_long_range_B_other 5.76 r_mcangle_it 5.098 r_mcangle_other 5.098 r_scangle_other 4.427 r_mcbond_it 3.674 r_mcbond_other 3.674 r_scbond_it 3.417 r_scbond_other 3.417 r_rigid_bond_restr 1.441 r_angle_refined_deg 1.238 r_angle_other_deg 0.988 r_chiral_restr 0.101 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 49340 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms 266
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing