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Yeast 20S proteasome in complex with 20
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 = 136.99 α = 90 b = 299.93 β = 113.23 c = 145.5 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 2016-06-18 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 0.071 11.4 3.1 274527
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 0.492 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 274527 14449 98.21 0.17673 0.17517 0.1801 0.20619 0.2081 RANDOM 66.927
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] 1.75 -1.07 -3.59 2.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.265 r_sphericity_free 32.317 r_sphericity_bonded 19.379 r_dihedral_angle_3_deg 15.412 r_dihedral_angle_4_deg 15.189 r_dihedral_angle_1_deg 5.75 r_long_range_B_refined 4.8 r_long_range_B_other 4.784 r_mcangle_it 4.196 r_mcangle_other 4.196
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.265 r_sphericity_free 32.317 r_sphericity_bonded 19.379 r_dihedral_angle_3_deg 15.412 r_dihedral_angle_4_deg 15.189 r_dihedral_angle_1_deg 5.75 r_long_range_B_refined 4.8 r_long_range_B_other 4.784 r_mcangle_it 4.196 r_mcangle_other 4.196 r_scangle_other 3.864 r_mcbond_it 3.079 r_mcbond_other 3.079 r_scbond_it 3.003 r_scbond_other 3.003 r_rigid_bond_restr 2.61 r_angle_refined_deg 1.164 r_angle_other_deg 0.889 r_chiral_restr 0.062 r_bond_refined_d 0.007 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 49304 Nucleic Acid Atoms Solvent Atoms 396 Heterogen Atoms 168
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC phasing REFMAC refinement