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Human 20S proteasome complex with Oprozomib 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 = 203.23 β = 90 c = 315.22 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 2015-11-10 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 2.19 170.81 99.3 0.078 1 15.2 7.15 351230
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 2.19 2.27 94.3 0.4 1.1
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 5LE5 2.19 170.81 351230 18458 99.4 0.1832 0.18121 0.1853 0.22169 0.2222 RANDOM 63.613
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] -0.72 0.15 0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.559 r_dihedral_angle_4_deg 17.835 r_dihedral_angle_3_deg 16.013 r_long_range_B_refined 9.545 r_long_range_B_other 9.545 r_dihedral_angle_1_deg 7.212 r_scangle_other 2.828 r_mcangle_it 2.05 r_mcangle_other 2.05 r_scbond_it 2.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.559 r_dihedral_angle_4_deg 17.835 r_dihedral_angle_3_deg 16.013 r_long_range_B_refined 9.545 r_long_range_B_other 9.545 r_dihedral_angle_1_deg 7.212 r_scangle_other 2.828 r_mcangle_it 2.05 r_mcangle_other 2.05 r_scbond_it 2.04 r_scbond_other 2.04 r_angle_refined_deg 1.746 r_angle_other_deg 1.31 r_mcbond_it 1.262 r_mcbond_other 1.261 r_chiral_restr 0.103 r_bond_refined_d 0.015 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 47840 Nucleic Acid Atoms Solvent Atoms 3717 Heterogen Atoms 324
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling