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Human 20S proteasome complex with Bortezomib at 2.1 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 = 113.37 α = 90 b = 202.72 β = 90 c = 314.9 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 2015-08-20 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 2.1 170.45 98.56 0.112 1 12.4 5.13 393306
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 2.1 2.2 89.1 0.26 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 2.1 170.45 393306 20644 98.56 0.18579 0.18372 0.1907 0.2255 0.2298 RANDOM 51.099
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] 0.61 -1.35 0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.368 r_dihedral_angle_4_deg 17.36 r_dihedral_angle_3_deg 15.559 r_long_range_B_refined 8.19 r_long_range_B_other 8.19 r_dihedral_angle_1_deg 7.248 r_scangle_other 2.621 r_mcangle_it 1.921 r_mcangle_other 1.921 r_angle_refined_deg 1.718
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.368 r_dihedral_angle_4_deg 17.36 r_dihedral_angle_3_deg 15.559 r_long_range_B_refined 8.19 r_long_range_B_other 8.19 r_dihedral_angle_1_deg 7.248 r_scangle_other 2.621 r_mcangle_it 1.921 r_mcangle_other 1.921 r_angle_refined_deg 1.718 r_scbond_it 1.718 r_scbond_other 1.718 r_angle_other_deg 1.263 r_mcbond_it 1.182 r_mcbond_other 1.182 r_chiral_restr 0.103 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 47877 Nucleic Acid Atoms Solvent Atoms 3674 Heterogen Atoms 379
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling