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Native human 20S proteasome in Mg-Acetate at 2.2 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 = 113.86 α = 90 b = 203.15 β = 90 c = 316.02 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 2015-11-09 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) 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 2.2 170.89 98.81 1 13 6.9 346869
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 2.28 99.4 0.36 0.9
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 FOURIER SYNTHESIS THROUGHOUT 5LE5 2.2 170.89 346869 18235 98.81 0.17922 0.17702 0.1807 0.2214 0.2226 RANDOM 65.884
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] 0.34 -1.71 1.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.469 r_dihedral_angle_4_deg 17.871 r_dihedral_angle_3_deg 15.72 r_long_range_B_refined 8.684 r_long_range_B_other 8.684 r_dihedral_angle_1_deg 7.253 r_scangle_other 3.103 r_scbond_it 2.228 r_scbond_other 2.228 r_mcangle_it 2.178
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.469 r_dihedral_angle_4_deg 17.871 r_dihedral_angle_3_deg 15.72 r_long_range_B_refined 8.684 r_long_range_B_other 8.684 r_dihedral_angle_1_deg 7.253 r_scangle_other 3.103 r_scbond_it 2.228 r_scbond_other 2.228 r_mcangle_it 2.178 r_mcangle_other 2.178 r_angle_refined_deg 1.755 r_mcbond_it 1.357 r_mcbond_other 1.357 r_angle_other_deg 1.303 r_chiral_restr 0.103 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.005 r_gen_planes_other 0.005 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 47812 Nucleic Acid Atoms Solvent Atoms 3331 Heterogen Atoms 159
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling