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Structure of Sir2Tm bound to a propionylated peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H4F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 Crystals were obtained from 1:1 mix of protein and the well solution (9.5% (w/v) PEG3350, 100 mM CHES buffer), pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.5 50.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.561 α = 90 b = 60.013 β = 90 c = 106.345 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 Bent conical Si-mirror (Rh coated) 2008-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.9002 APS 14-BM-C
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 1.8 30.01 99.82 0.099 23.8 7 28402 28346 2 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) 1.8 1.85 99.3 0.639 2.9 6.5
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 2H4F 1.8 30.01 28402 26911 1430 99.82 0.16715 0.16493 0.1728 0.2101 0.2134 RANDOM 16.398
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] 0.63 0.21 -0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.892 r_dihedral_angle_4_deg 20.086 r_dihedral_angle_3_deg 13.696 r_dihedral_angle_1_deg 6.757 r_scangle_it 4.117 r_scbond_it 2.869 r_mcangle_it 1.828 r_angle_refined_deg 1.612 r_mcbond_it 1.19 r_angle_other_deg 0.951
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.892 r_dihedral_angle_4_deg 20.086 r_dihedral_angle_3_deg 13.696 r_dihedral_angle_1_deg 6.757 r_scangle_it 4.117 r_scbond_it 2.869 r_mcangle_it 1.828 r_angle_refined_deg 1.612 r_mcbond_it 1.19 r_angle_other_deg 0.951 r_mcbond_other 0.443 r_chiral_restr 0.115 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1958 Nucleic Acid Atoms Solvent Atoms 247 Heterogen Atoms 1
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling