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Native human 20S proteasome at 1.8 Angstrom
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UNE
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 2.62 53.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.44 α = 90 b = 202.77 β = 90 c = 316 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 1.8 170.66 99.9 0.091 1 18.5 13.4 633728
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 99.5 2.91 0.32 0.91 11
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 3UNE 1.8 170.66 633728 33221 99.91 0.18358 0.18211 0.1898 0.21175 0.2167 RANDOM 45.666
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 0.11 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.057 r_dihedral_angle_4_deg 16.877 r_dihedral_angle_3_deg 15.518 r_long_range_B_refined 7.679 r_long_range_B_other 7.679 r_dihedral_angle_1_deg 6.837 r_scangle_other 2.376 r_angle_refined_deg 1.778 r_scbond_it 1.651 r_scbond_other 1.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.057 r_dihedral_angle_4_deg 16.877 r_dihedral_angle_3_deg 15.518 r_long_range_B_refined 7.679 r_long_range_B_other 7.679 r_dihedral_angle_1_deg 6.837 r_scangle_other 2.376 r_angle_refined_deg 1.778 r_scbond_it 1.651 r_scbond_other 1.65 r_mcangle_it 1.626 r_mcangle_other 1.626 r_angle_other_deg 1.342 r_mcbond_it 0.996 r_mcbond_other 0.996 r_chiral_restr 0.115 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.006 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 48194 Nucleic Acid Atoms Solvent Atoms 3512 Heterogen Atoms 217
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing