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Crystal structure of zebrafish Sirtuin 5 in complex with 2R-butyl- 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 7.2 20% PEG3350, 0.1 M HEPES PH 7.2
Crystal Properties Matthews coefficient Solvent content 2.9 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.44 α = 90 b = 87.44 β = 90 c = 315.06 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 MIRROR 2013-07-05 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 2.9 50 99.9 0.17 13.3 8.1 16737 2
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 2.9 3 99.9 1.01 1.9 6.4
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 2.9 48.44 15861 876 99.9 0.20549 0.20279 0.206 0.25387 0.2553 RANDOM 52.573
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] 0.05 0.02 0.05 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.939 r_dihedral_angle_4_deg 18.135 r_dihedral_angle_3_deg 17.929 r_dihedral_angle_1_deg 6.347 r_mcangle_it 2.878 r_scbond_it 1.914 r_mcbond_other 1.667 r_mcbond_it 1.666 r_angle_refined_deg 1.558 r_angle_other_deg 1.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.939 r_dihedral_angle_4_deg 18.135 r_dihedral_angle_3_deg 17.929 r_dihedral_angle_1_deg 6.347 r_mcangle_it 2.878 r_scbond_it 1.914 r_mcbond_other 1.667 r_mcbond_it 1.666 r_angle_refined_deg 1.558 r_angle_other_deg 1.112 r_chiral_restr 0.078 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.005 r_gen_planes_other 0.004 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 4137 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing