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SIRT2-H187A structure in complex with H3K18myr peptide and native NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4X3O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 289 0.1 M MES 5.5, 9.2% PEG10000
Crystal Properties Matthews coefficient Solvent content 2.21 44.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.434 α = 100.187 b = 48.13 β = 91.579 c = 96.194 γ = 112.167
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 PILATUS3 6M 2025-04-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97861 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.41 47.13 92.1 0.995 8.9 3.7 21638
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.41 2.5 0.809
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4X3O 2.41 47.129 21622 1083 92.056 0.201 0.1976 0.2069 0.2733 0.2807 46.165
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] -0.979 0.71 -2.658 -0.164 -4.357 3.359
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.773 r_dihedral_angle_6_deg 14.016 r_dihedral_angle_2_deg 10.863 r_lrange_it 8.807 r_lrange_other 8.807 r_dihedral_angle_1_deg 7.756 r_scangle_it 6.16 r_scangle_other 6.159 r_mcangle_it 5.889 r_mcangle_other 5.889
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.773 r_dihedral_angle_6_deg 14.016 r_dihedral_angle_2_deg 10.863 r_lrange_it 8.807 r_lrange_other 8.807 r_dihedral_angle_1_deg 7.756 r_scangle_it 6.16 r_scangle_other 6.159 r_mcangle_it 5.889 r_mcangle_other 5.889 r_scbond_it 3.957 r_scbond_other 3.956 r_mcbond_it 3.894 r_mcbond_other 3.893 r_angle_refined_deg 1.656 r_dihedral_angle_other_2_deg 0.842 r_angle_other_deg 0.568 r_symmetry_xyhbond_nbd_refined 0.296 r_nbd_other 0.24 r_nbd_refined 0.22 r_symmetry_nbd_refined 0.212 r_symmetry_nbd_other 0.207 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.158 r_symmetry_xyhbond_nbd_other 0.113 r_symmetry_nbtor_other 0.088 r_chiral_restr 0.077 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4571 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 120
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing