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Human Sirt5 in complex with stalled peptidylimidate intermediate of inhibitory compound 29
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RIY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 30% PEG3350, 0.2 M NaCl, 0.1 M Bis-Tris pH 5.5, 5% 1,3-butandiol
Crystal Properties Matthews coefficient Solvent content 2.27 45.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.326 α = 97.39 b = 55.969 β = 99.29 c = 123.034 γ = 90.52
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 2M-F 2016-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.000030 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.32 43.77 91.5 0.059 0.999 6.8 2 227669
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.32 1.4 88.1 0.959 0.723 1.1 1.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3RIY 1.32 43.77 224952 2388 91.87 0.16076 0.16025 0.20856 0.2093 RANDOM 21.373
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] -2.34 3.38 -2.91 -1.76 0.81 4.1
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 47.72 r_dihedral_angle_2_deg 34.612 r_dihedral_angle_4_deg 20.43 r_sphericity_bonded 19.296 r_dihedral_angle_3_deg 13.724 r_long_range_B_refined 9.451 r_long_range_B_other 9.451 r_mcangle_it 8.762 r_mcangle_other 8.762 r_scangle_other 7.766
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 47.72 r_dihedral_angle_2_deg 34.612 r_dihedral_angle_4_deg 20.43 r_sphericity_bonded 19.296 r_dihedral_angle_3_deg 13.724 r_long_range_B_refined 9.451 r_long_range_B_other 9.451 r_mcangle_it 8.762 r_mcangle_other 8.762 r_scangle_other 7.766 r_mcbond_it 7.279 r_mcbond_other 7.278 r_scbond_it 7.102 r_scbond_other 7.101 r_rigid_bond_restr 6.781 r_dihedral_angle_1_deg 6.418 r_angle_refined_deg 2.886 r_angle_other_deg 1.801 r_chiral_restr 0.276 r_bond_refined_d 0.031 r_gen_planes_refined 0.017 r_gen_planes_other 0.01 r_bond_other_d 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8313 Nucleic Acid Atoms Solvent Atoms 1086 Heterogen Atoms 440
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing