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SIRT2 structure in complex with H3K18myr peptide: pre NAD binding state
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 8 289 Tris 8.0, 25% PEG2000MME
Crystal Properties Matthews coefficient Solvent content 1.95 36.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.508 α = 90 b = 72.528 β = 95.27 c = 53.921 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 PIXEL DECTRIS PILATUS 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 2.15 53.751 99 0.997 11.9 6.9 14755
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 2.15 2.21 0.876
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 2.15 53.751 14728 739 98.779 0.199 0.1963 0.2033 0.2511 0.2457 47.31
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] -2.939 0.346 -0.407 3.227
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.952 r_dihedral_angle_3_deg 16.94 r_dihedral_angle_6_deg 14.464 r_dihedral_angle_1_deg 6.634 r_lrange_other 3.516 r_lrange_it 3.514 r_scangle_it 2.274 r_scangle_other 2.274 r_mcangle_it 2.142 r_mcangle_other 2.142
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.952 r_dihedral_angle_3_deg 16.94 r_dihedral_angle_6_deg 14.464 r_dihedral_angle_1_deg 6.634 r_lrange_other 3.516 r_lrange_it 3.514 r_scangle_it 2.274 r_scangle_other 2.274 r_mcangle_it 2.142 r_mcangle_other 2.142 r_angle_refined_deg 1.573 r_scbond_it 1.537 r_scbond_other 1.536 r_mcbond_it 1.511 r_mcbond_other 1.51 r_angle_other_deg 0.528 r_nbd_other 0.264 r_symmetry_xyhbond_nbd_refined 0.263 r_symmetry_nbd_other 0.217 r_xyhbond_nbd_other 0.217 r_nbd_refined 0.213 r_xyhbond_nbd_refined 0.2 r_symmetry_nbd_refined 0.187 r_nbtor_refined 0.181 r_metal_ion_refined 0.139 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.069 r_symmetry_xyhbond_nbd_other 0.049 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 2311 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PARROT phasing