☰ Navigation Tabs
Crystal structure of zebrafish Sirtuin 5 in complex with 3-(phenylthio)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 2.69 54.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.22 α = 90 b = 87.22 β = 90 c = 318.85 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 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 3.3 50 99.5 0.393 0.938 5 4.1 10989
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 3.3 3.39 99.3 1.218 0.496 1.4 4.3
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 3.3 48.73 10922 573 98.97 0.22517 0.22189 0.2269 0.28431 0.2879 RANDOM 61.295
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] -0.65 -0.32 -0.65 2.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.172 r_dihedral_angle_4_deg 20.611 r_dihedral_angle_3_deg 19.533 r_dihedral_angle_1_deg 7.286 r_long_range_B_refined 5.182 r_long_range_B_other 5.182 r_mcangle_it 2.841 r_mcangle_other 2.841 r_scangle_other 2.533 r_angle_refined_deg 1.695
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.172 r_dihedral_angle_4_deg 20.611 r_dihedral_angle_3_deg 19.533 r_dihedral_angle_1_deg 7.286 r_long_range_B_refined 5.182 r_long_range_B_other 5.182 r_mcangle_it 2.841 r_mcangle_other 2.841 r_scangle_other 2.533 r_angle_refined_deg 1.695 r_mcbond_it 1.6 r_mcbond_other 1.6 r_scbond_it 1.507 r_scbond_other 1.507 r_angle_other_deg 1.037 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.003 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 4282 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing