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Sirtuin 5 from Danio rerio in complex with 3-hydroxy-3-methylglutaryl-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 7.6 293 0.1 M HEPES pH 7.6
20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.92 57.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.54 α = 90 b = 87.54 β = 90 c = 316.92 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 Sagitally bended Si111-crystal 2015-09-08 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) R Merge I (Observed) 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 3.1 50 99.9 0.248 0.994 10.2 10.3 13919
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.2 99.9 1.512 0.598 1.6 10.8
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 3.1 48.67 13206 713 99.9 0.2 0.196 0.2062 0.266 0.2715 RANDOM 71.83
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] -0.38 -0.19 -0.38 1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.868 r_dihedral_angle_4_deg 18.215 r_dihedral_angle_3_deg 15.862 r_dihedral_angle_1_deg 6.567 r_long_range_B_refined 5.102 r_long_range_B_other 5.098 r_mcangle_it 2.912 r_mcangle_other 2.911 r_scangle_other 2.885 r_scbond_it 1.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.868 r_dihedral_angle_4_deg 18.215 r_dihedral_angle_3_deg 15.862 r_dihedral_angle_1_deg 6.567 r_long_range_B_refined 5.102 r_long_range_B_other 5.098 r_mcangle_it 2.912 r_mcangle_other 2.911 r_scangle_other 2.885 r_scbond_it 1.89 r_scbond_other 1.889 r_mcbond_it 1.677 r_mcbond_other 1.676 r_angle_refined_deg 1.539 r_angle_other_deg 1.109 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.003 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 4215 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing