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Yeast 20S proteasome with human beta2i (1-53) in complex with 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 = 135.77 α = 90 b = 299.59 β = 113.24 c = 144.64 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 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 2.7 50 98.7 0.089 8.7 3.1 286280
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 2.7 2.8 99.7 0.529 2.1
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 2.7 15 270398 14231 98.29 0.1926 0.19124 0.1956 0.21868 0.2204 RANDOM 68.037
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] 2.34 0.27 -5.44 2.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.278 r_sphericity_free 32.601 r_dihedral_angle_3_deg 14.649 r_dihedral_angle_4_deg 14.142 r_dihedral_angle_1_deg 5.818 r_sphericity_bonded 5.741 r_long_range_B_refined 3.275 r_long_range_B_other 3.231 r_mcangle_it 2.753 r_mcangle_other 2.753
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.278 r_sphericity_free 32.601 r_dihedral_angle_3_deg 14.649 r_dihedral_angle_4_deg 14.142 r_dihedral_angle_1_deg 5.818 r_sphericity_bonded 5.741 r_long_range_B_refined 3.275 r_long_range_B_other 3.231 r_mcangle_it 2.753 r_mcangle_other 2.753 r_scangle_other 2.438 r_mcbond_it 2.047 r_mcbond_other 2.047 r_scbond_it 1.996 r_scbond_other 1.995 r_rigid_bond_restr 1.287 r_angle_refined_deg 1.188 r_angle_other_deg 0.908 r_chiral_restr 0.068 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 636 Heterogen Atoms 190
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC phasing REFMAC refinement