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Human 20S proteasome complex with Oprozomib at 1.9 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 = 113.39 α = 90 b = 202.65 β = 90 c = 315.14 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 1.9 170.45 97.5 0.087 1 15.3 5.04 526170
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 1.9 2 99.4 0.24 0.83
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 1.9 170.45 526170 27607 97.82 0.18967 0.18783 0.22508 0.1994 RANDOM 49.054
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] -1.68 0.87 0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.203 r_dihedral_angle_4_deg 18.26 r_dihedral_angle_3_deg 15.716 r_long_range_B_refined 8.391 r_long_range_B_other 8.391 r_dihedral_angle_1_deg 7.411 r_scangle_other 2.718 r_angle_refined_deg 1.971 r_scbond_it 1.903 r_scbond_other 1.903
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.203 r_dihedral_angle_4_deg 18.26 r_dihedral_angle_3_deg 15.716 r_long_range_B_refined 8.391 r_long_range_B_other 8.391 r_dihedral_angle_1_deg 7.411 r_scangle_other 2.718 r_angle_refined_deg 1.971 r_scbond_it 1.903 r_scbond_other 1.903 r_mcangle_it 1.878 r_mcangle_other 1.878 r_angle_other_deg 1.41 r_mcbond_it 1.169 r_mcbond_other 1.169 r_chiral_restr 0.128 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.007 r_gen_planes_other 0.006 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 47836 Nucleic Acid Atoms Solvent Atoms 3542 Heterogen Atoms 292
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling