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Sir2-deacetylated peptide (from enzymatic turnover in crystal)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YC5 PDB Entry: 1yc5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9.6 293 CHES, PEG3350, PH9.6, acetylated peptide. Crystals were soaked in cryo + 5mM NAD, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.49 50.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.049 α = 90 b = 59.683 β = 90 c = 107.35 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 315 2005-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C APS 14-BM-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.1 50 99.9 0.092 20.3 6.9 17933 16973 2 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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: 1yc5 2.1 50 2 16886 16973 913 99.94 0.19999 0.19762 0.1979 0.24619 0.2474 RANDOM 30.982
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] 0.39 0.08 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.645 r_dihedral_angle_4_deg 19.404 r_dihedral_angle_3_deg 13.714 r_sphericity_free 7.971 r_dihedral_angle_1_deg 6.467 r_scangle_it 4.765 r_rigid_bond_restr 4.503 r_scbond_it 4.39 r_sphericity_bonded 3.349 r_mcangle_it 2.394
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.645 r_dihedral_angle_4_deg 19.404 r_dihedral_angle_3_deg 13.714 r_sphericity_free 7.971 r_dihedral_angle_1_deg 6.467 r_scangle_it 4.765 r_rigid_bond_restr 4.503 r_scbond_it 4.39 r_sphericity_bonded 3.349 r_mcangle_it 2.394 r_angle_refined_deg 1.744 r_mcbond_it 1.612 r_nbtor_refined 0.302 r_nbd_refined 0.227 r_symmetry_hbond_refined 0.16 r_symmetry_vdw_refined 0.158 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.11 r_bond_refined_d 0.019 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1936 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data scaling CNS phasing