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SIRT2 structure in complex with H3K18myr peptide and native NAD: pre-catalysis state 3
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% PEG 2000MME
Crystal Properties Matthews coefficient Solvent content 2.26 45.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.76 α = 90 b = 76.57 β = 97.881 c = 55.94 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 PILATUS3 6M 2024-10-29 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 1.86 44.93 90.8 0.999 10.4 5.8 31715
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 1.86 1.9 0.29
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.86 44.93 26214 1306 98.738 0.188 0.1858 0.1969 0.2314 0.2413 40.033
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] 1.25 0.928 -0.504 -0.967
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.16 r_dihedral_angle_6_deg 14.691 r_dihedral_angle_2_deg 8.929 r_lrange_it 8.545 r_lrange_other 8.5 r_dihedral_angle_1_deg 6.949 r_scangle_it 6.284 r_scangle_other 6.282 r_mcangle_it 4.941 r_mcangle_other 4.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.16 r_dihedral_angle_6_deg 14.691 r_dihedral_angle_2_deg 8.929 r_lrange_it 8.545 r_lrange_other 8.5 r_dihedral_angle_1_deg 6.949 r_scangle_it 6.284 r_scangle_other 6.282 r_mcangle_it 4.941 r_mcangle_other 4.94 r_scbond_it 4.349 r_scbond_other 4.348 r_mcbond_it 3.593 r_mcbond_other 3.587 r_angle_refined_deg 1.846 r_dihedral_angle_other_2_deg 0.66 r_angle_other_deg 0.614 r_nbd_refined 0.237 r_nbd_other 0.223 r_symmetry_nbd_other 0.205 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.179 r_symmetry_nbd_refined 0.144 r_metal_ion_refined 0.14 r_symmetry_xyhbond_nbd_refined 0.131 r_symmetry_xyhbond_nbd_other 0.098 r_chiral_restr 0.087 r_symmetry_nbtor_other 0.086 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2442 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing