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Crystal structure of zebrafish Sirtuin 5 in complex with succinylated CPS1-peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NYR PDB ENTRY 2NYR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.4 20% PEG3350, 0.1 M HEPES PH 7.4
Crystal Properties Matthews coefficient Solvent content 2.86 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.44 α = 90 b = 87.44 β = 90 c = 314.92 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 CCD MARMOSAIC 225 mm CCD MIRROR 2012-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3 100 99.9 0.18 11.2 8.1 15155 1.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.1 99.9 1.34 1.7 8.5
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 PDB ENTRY 2NYR 3 75.73 14400 758 99.89 0.21782 0.2152 0.2194 0.26672 0.2453 RANDOM 70.934
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] 0.71 0.35 0.71 -2.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.961 r_dihedral_angle_4_deg 18.357 r_dihedral_angle_3_deg 16.09 r_dihedral_angle_1_deg 6.624 r_mcangle_it 3.73 r_scbond_it 2.567 r_mcbond_it 2.251 r_mcbond_other 2.251 r_angle_refined_deg 1.673 r_angle_other_deg 1.151
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.961 r_dihedral_angle_4_deg 18.357 r_dihedral_angle_3_deg 16.09 r_dihedral_angle_1_deg 6.624 r_mcangle_it 3.73 r_scbond_it 2.567 r_mcbond_it 2.251 r_mcbond_other 2.251 r_angle_refined_deg 1.673 r_angle_other_deg 1.151 r_chiral_restr 0.1 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.003 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4162 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing