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SIRT2 structure in complex with H3K18myr peptide and native NAD: pre-catalysis state 1
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 289 Tris 8.0, 25% PEG 2000MME
Crystal Properties Matthews coefficient Solvent content 2.36 47.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.859 α = 90 b = 76.409 β = 97.293 c = 55.64 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 2.57 55.251 99.2 0.991 7.1 6.9 10021
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 2.57 2.68 0.767
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 2.57 55.251 9950 495 98.417 0.19 0.1867 0.192 0.2642 0.2692 46.722
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] -0.424 0.588 0.768 -0.479
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.703 r_dihedral_angle_6_deg 13.025 r_dihedral_angle_1_deg 7.145 r_dihedral_angle_2_deg 7.023 r_lrange_it 5.081 r_lrange_other 5.08 r_scangle_it 2.79 r_scangle_other 2.789 r_mcangle_it 2.574 r_mcangle_other 2.573
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.703 r_dihedral_angle_6_deg 13.025 r_dihedral_angle_1_deg 7.145 r_dihedral_angle_2_deg 7.023 r_lrange_it 5.081 r_lrange_other 5.08 r_scangle_it 2.79 r_scangle_other 2.789 r_mcangle_it 2.574 r_mcangle_other 2.573 r_scbond_it 1.773 r_scbond_other 1.772 r_mcbond_it 1.556 r_mcbond_other 1.556 r_angle_refined_deg 1.498 r_angle_other_deg 0.513 r_dihedral_angle_other_2_deg 0.46 r_nbd_refined 0.224 r_nbd_other 0.21 r_symmetry_nbd_other 0.209 r_metal_ion_refined 0.196 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.161 r_symmetry_xyhbond_nbd_refined 0.159 r_symmetry_nbd_refined 0.158 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.064 r_symmetry_xyhbond_nbd_other 0.046 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2266 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing