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Zebrafish Sirt5 in complex with stalled peptidylimidate and bicyclic intermediate of inhibitory compound 29
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4UTV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 20% PEG8000, 0.2 M MgCl2, 0.1 M Tris/HCl pH 8.5, 0.1 M glycine
Crystal Properties Matthews coefficient Solvent content 2.11 41.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.93 α = 90 b = 113.59 β = 103.24 c = 72.31 γ = 90
Symmetry Space Group P 1 21 1
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 2016-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.918400 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 2.4 50 96.2 0.252 0.989 6.1 3.8 38453
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 2.4 2.5 97.3 1.702 0.517 0.9 3.8
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 4UTV 2.4 48.41 36530 1923 96.26 0.25531 0.25263 0.2569 0.30492 0.3033 RANDOM 52.227
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] 0.83 1.44 -1.63 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.805 r_dihedral_angle_3_deg 18.062 r_dihedral_angle_4_deg 16.815 r_dihedral_angle_1_deg 6.542 r_long_range_B_refined 6.122 r_long_range_B_other 6.115 r_mcangle_it 3.328 r_mcangle_other 3.328 r_scangle_other 3.078 r_mcbond_it 2.032
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.805 r_dihedral_angle_3_deg 18.062 r_dihedral_angle_4_deg 16.815 r_dihedral_angle_1_deg 6.542 r_long_range_B_refined 6.122 r_long_range_B_other 6.115 r_mcangle_it 3.328 r_mcangle_other 3.328 r_scangle_other 3.078 r_mcbond_it 2.032 r_mcbond_other 2.032 r_scbond_it 1.983 r_scbond_other 1.983 r_angle_refined_deg 1.967 r_angle_other_deg 1.3 r_chiral_restr 0.1 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.005 r_gen_planes_other 0.002 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 8541 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms 420
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing