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The structure of Sir2Af1 bound to a succinylated histone peptide
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, HANGING DROP 8.5 293 0.1 M Tris pH 8.5, 200 mM MgCl2, and 20% (w/v) PEG 8,000
Crystal Properties Matthews coefficient Solvent content 2.24 45.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.61 α = 90 b = 51.362 β = 101.85 c = 57.687 γ = 90
Symmetry Space Group P 1 21 1
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 RIGAKU SATURN 944+ 2014-01-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54
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 1.79 21.94 95.39 0.1172 7.36 2.3 53220 23269
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 1.79 1.849 83.73 1.85 1.5
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 1ICI 1.79 21.94 22073 1196 95.33 0.19374 0.19224 0.2009 0.22113 0.2314 RANDOM 19.4
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] -1.15 -0.11 0.36 0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.933 r_dihedral_angle_4_deg 13.159 r_dihedral_angle_3_deg 11.742 r_dihedral_angle_1_deg 4.649 r_angle_refined_deg 1.002 r_angle_other_deg 0.717 r_chiral_restr 0.056 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.933 r_dihedral_angle_4_deg 13.159 r_dihedral_angle_3_deg 11.742 r_dihedral_angle_1_deg 4.649 r_angle_refined_deg 1.002 r_angle_other_deg 0.717 r_chiral_restr 0.056 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it 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 1932 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement