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SIRT2-F96A structure in complex with H3K18myr peptide and native NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9VEM
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 2.31 46.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.915 α = 90 b = 77.134 β = 97.107 c = 56.155 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 EIGER X 16M 2024-12-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.97918 SSRF BL10U2
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 2.34 45.21 91.2 0.995 15.3 5.3 12400
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 2.34 2.42 0.965
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 9VEM 2.34 45.21 12377 567 90.894 0.181 0.1788 0.2356 0.2462 43.592
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] 1.209 2.402 -0.756 -1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.268 r_dihedral_angle_6_deg 14.71 r_dihedral_angle_2_deg 9.027 r_dihedral_angle_1_deg 6.871 r_lrange_it 6.811 r_lrange_other 6.811 r_scangle_it 5.205 r_scangle_other 5.203 r_mcangle_it 3.458 r_mcangle_other 3.457
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.268 r_dihedral_angle_6_deg 14.71 r_dihedral_angle_2_deg 9.027 r_dihedral_angle_1_deg 6.871 r_lrange_it 6.811 r_lrange_other 6.811 r_scangle_it 5.205 r_scangle_other 5.203 r_mcangle_it 3.458 r_mcangle_other 3.457 r_scbond_it 3.393 r_scbond_other 3.392 r_mcbond_it 2.372 r_mcbond_other 2.37 r_angle_refined_deg 1.754 r_angle_other_deg 0.572 r_dihedral_angle_other_2_deg 0.241 r_nbd_other 0.229 r_nbd_refined 0.227 r_symmetry_nbd_other 0.207 r_xyhbond_nbd_refined 0.195 r_metal_ion_refined 0.195 r_nbtor_refined 0.185 r_symmetry_xyhbond_nbd_refined 0.145 r_symmetry_nbd_refined 0.137 r_symmetry_nbtor_other 0.091 r_chiral_restr 0.077 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2334 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing