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Crystal structure of zebrafish Sirtuin 5 in complex with 3-(benzylthio)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 7.5 293 0.1 M HEPES pH 7.4, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.63 53.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.134 α = 90 b = 87.134 β = 90 c = 316.677 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 2M MIRRORS 2016-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918409 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 2.98 50 99.8 0.358 0.994 9.8 15.5 15459
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 2.98 3.16 99.1 2.1 0.513 1.3 16
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 2.98 48.51 14686 773 99.77 0.20163 0.19785 0.2029 0.27485 0.2779 RANDOM 67.667
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] 0.22 0.11 0.22 -0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.391 r_dihedral_angle_4_deg 20.627 r_dihedral_angle_3_deg 18.049 r_long_range_B_refined 7.586 r_long_range_B_other 7.583 r_dihedral_angle_1_deg 6.543 r_scangle_other 5.166 r_mcangle_it 4.998 r_mcangle_other 4.997 r_scbond_it 3.182
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.391 r_dihedral_angle_4_deg 20.627 r_dihedral_angle_3_deg 18.049 r_long_range_B_refined 7.586 r_long_range_B_other 7.583 r_dihedral_angle_1_deg 6.543 r_scangle_other 5.166 r_mcangle_it 4.998 r_mcangle_other 4.997 r_scbond_it 3.182 r_scbond_other 3.182 r_mcbond_it 3.015 r_mcbond_other 3.015 r_angle_refined_deg 1.872 r_angle_other_deg 1.099 r_chiral_restr 0.1 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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 4232 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing