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Yeast 20S proteasome in complex with 5 (7- and 6-membered ring)
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 = 136.63 α = 90 b = 301.8 β = 113.06 c = 145.57 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 2014-09-07 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 2.7 50 97.9 0.074 12.5 3.1 290007
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 98.6 0.552 2.4
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 273927 14418 97.48 0.18327 0.18145 0.187 0.21774 0.2216 RANDOM 61.376
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] 2.72 -0.08 -3.62 0.72
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 41.163 r_dihedral_angle_2_deg 34.74 r_sphericity_bonded 17.418 r_dihedral_angle_3_deg 14.407 r_dihedral_angle_4_deg 14.372 r_dihedral_angle_1_deg 5.352 r_long_range_B_refined 4.319 r_long_range_B_other 4.306 r_mcangle_it 3.666 r_mcangle_other 3.666
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 41.163 r_dihedral_angle_2_deg 34.74 r_sphericity_bonded 17.418 r_dihedral_angle_3_deg 14.407 r_dihedral_angle_4_deg 14.372 r_dihedral_angle_1_deg 5.352 r_long_range_B_refined 4.319 r_long_range_B_other 4.306 r_mcangle_it 3.666 r_mcangle_other 3.666 r_scangle_other 3.426 r_mcbond_it 2.723 r_mcbond_other 2.723 r_scbond_it 2.713 r_scbond_other 2.713 r_angle_refined_deg 1.056 r_rigid_bond_restr 0.99 r_angle_other_deg 0.888 r_chiral_restr 0.057 r_bond_refined_d 0.006 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 49376 Nucleic Acid Atoms Solvent Atoms 544 Heterogen Atoms 218
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing