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Crystal structure of zebrafish Sirtuin 5 in complex with 3(S)-(naphthylthio)succinyl-CPS1 peptide
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, HANGING DROP 7.7 293 0.1 M HEPES 7.7, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.7 54.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87 α = 90 b = 87 β = 90 c = 316.88 γ = 120
Symmetry Space Group P 65 2 2
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 2017-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918400 BESSY 14.1
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 2.5 20 99.6 0.351 0.995 7.2 10.6 25573
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 2.5 2.56 99.9 8.224 0.128 0.3 11.1
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 MOLECULAR REPLACEMENT THROUGHOUT 4utv 2.5 19.85 24278 1279 99.56 0.24513 0.24158 0.2447 0.31055 0.3086 RANDOM 78.898
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 0.36 0.72 -2.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.593 r_dihedral_angle_3_deg 15.694 r_dihedral_angle_4_deg 11.918 r_long_range_B_refined 8.465 r_long_range_B_other 8.464 r_dihedral_angle_1_deg 6.663 r_mcangle_it 5.727 r_mcangle_other 5.726 r_scangle_other 5.127 r_mcbond_it 3.379
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.593 r_dihedral_angle_3_deg 15.694 r_dihedral_angle_4_deg 11.918 r_long_range_B_refined 8.465 r_long_range_B_other 8.464 r_dihedral_angle_1_deg 6.663 r_mcangle_it 5.727 r_mcangle_other 5.726 r_scangle_other 5.127 r_mcbond_it 3.379 r_mcbond_other 3.379 r_scbond_it 3.034 r_scbond_other 3.034 r_angle_refined_deg 1.331 r_angle_other_deg 0.958 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 4204 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing