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Crystal structure of human Sirt2 in complex with a brominated 2nd generation SirReal inhibitor and NAD+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RMG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 278 27 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.96 58.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.303 α = 90 b = 55.432 β = 114.91 c = 96.176 γ = 90
Symmetry Space Group I 1 2 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 PIXEL DECTRIS PILATUS 6M 2014-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 1.77 46.78 98.2 0.095 10.3 6.7 38622
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 1.77 1.81 98.1 2.05 1 6.9
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 4RMG 1.77 46.78 36691 1913 97.9 0.17686 0.17494 0.1875 0.21286 0.2254 RANDOM 33.455
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] -1.09 -1 1.34 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.249 r_dihedral_angle_4_deg 16.205 r_dihedral_angle_3_deg 12.633 r_dihedral_angle_1_deg 6.155 r_long_range_B_refined 5.088 r_long_range_B_other 5.027 r_scangle_other 3.101 r_mcangle_it 2.421 r_mcangle_other 2.421 r_scbond_it 1.897
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.249 r_dihedral_angle_4_deg 16.205 r_dihedral_angle_3_deg 12.633 r_dihedral_angle_1_deg 6.155 r_long_range_B_refined 5.088 r_long_range_B_other 5.027 r_scangle_other 3.101 r_mcangle_it 2.421 r_mcangle_other 2.421 r_scbond_it 1.897 r_scbond_other 1.896 r_angle_refined_deg 1.646 r_mcbond_it 1.484 r_mcbond_other 1.484 r_angle_other_deg 1.021 r_chiral_restr 0.098 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2391 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing