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Human 20S proteasome complex with Dihydroeponemycin at 2.0 Angstrom
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LE5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 0.1 M Bis-Tris,
0.2 M Magnesium Chloride,
10 % PEG3350
Crystal Properties Matthews coefficient Solvent content 2.54 51.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.89 α = 90 b = 203.49 β = 90 c = 316.04 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS 6M-F CRL Transfocator 2015-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9763 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2 171.09 99.5 0.094 1 12.2 9.43 464668
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 98.3 0.39 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 5LE5 2 171.09 464668 24379 99.52 0.1796 0.17788 0.21275 0.2096 RANDOM 49.785
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] -0.51 0.74 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.973 r_dihedral_angle_4_deg 17.929 r_dihedral_angle_3_deg 15.403 r_long_range_B_refined 8.133 r_long_range_B_other 8.133 r_dihedral_angle_1_deg 7.093 r_scangle_other 2.509 r_angle_refined_deg 1.724 r_mcangle_it 1.721 r_mcangle_other 1.721
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.973 r_dihedral_angle_4_deg 17.929 r_dihedral_angle_3_deg 15.403 r_long_range_B_refined 8.133 r_long_range_B_other 8.133 r_dihedral_angle_1_deg 7.093 r_scangle_other 2.509 r_angle_refined_deg 1.724 r_mcangle_it 1.721 r_mcangle_other 1.721 r_scbond_it 1.694 r_scbond_other 1.694 r_angle_other_deg 1.283 r_mcbond_it 1.057 r_mcbond_other 1.057 r_chiral_restr 0.109 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.005 r_gen_planes_other 0.004 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 47874 Nucleic Acid Atoms Solvent Atoms 3621 Heterogen Atoms 384
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling