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Crystal Structure of Human Sirtuin homolog 5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ICI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 273 18% PEG 4000, 0.1M Hepes, pH 7.5, 10% Isopropanol, VAPOR DIFFUSION, SITTING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 2.4 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.574 α = 93.5 b = 58.756 β = 92.75 c = 104.965 γ = 94.98
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 4 2005-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 0.9797 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.9 40.3 96.1 79819 79819
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 1.97 85.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1ICI 1.9 40.3 75815 75815 3994 95.46 0.18527 0.18259 0.1855 0.23604 0.1886 RANDOM 25.677
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] -0.5 -0.55 0.21 1.34 -0.17 -0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.436 r_dihedral_angle_4_deg 17.849 r_dihedral_angle_3_deg 15.476 r_dihedral_angle_1_deg 6.086 r_scangle_it 4.14 r_scbond_it 2.879 r_angle_refined_deg 1.822 r_mcangle_it 1.62 r_mcbond_it 1.059 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.436 r_dihedral_angle_4_deg 17.849 r_dihedral_angle_3_deg 15.476 r_dihedral_angle_1_deg 6.086 r_scangle_it 4.14 r_scbond_it 2.879 r_angle_refined_deg 1.822 r_mcangle_it 1.62 r_mcbond_it 1.059 r_nbtor_refined 0.303 r_symmetry_hbond_refined 0.21 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.178 r_xyhbond_nbd_refined 0.161 r_chiral_restr 0.125 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8015 Nucleic Acid Atoms Solvent Atoms 707 Heterogen Atoms 208
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASES phasing