☰ Navigation Tabs
SIRT2 structure in complex with H3K18myr peptide
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 2.08 40.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.152 α = 90 b = 73.504 β = 94.087 c = 55.731 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 2024-06-17 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 1.61 55.59 91.8 0.997 17.1 6.4 34600
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 1.61 1.64 0.939
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 4X3O 1.61 27.81 34572 1746 91.681 0.191 0.1883 0.2313 0.2549 25.83
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] -0.348 1.88 -0.606 0.678
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.277 r_dihedral_angle_4_deg 20.29 r_dihedral_angle_3_deg 15.832 r_dihedral_angle_1_deg 6.812 r_lrange_it 4.896 r_lrange_other 4.882 r_scangle_it 3.226 r_scangle_other 3.226 r_scbond_it 2.168 r_scbond_other 2.167
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.277 r_dihedral_angle_4_deg 20.29 r_dihedral_angle_3_deg 15.832 r_dihedral_angle_1_deg 6.812 r_lrange_it 4.896 r_lrange_other 4.882 r_scangle_it 3.226 r_scangle_other 3.226 r_scbond_it 2.168 r_scbond_other 2.167 r_mcangle_it 1.993 r_mcangle_other 1.993 r_angle_refined_deg 1.903 r_angle_other_deg 1.49 r_mcbond_it 1.39 r_mcbond_other 1.388 r_nbd_refined 0.238 r_nbd_other 0.192 r_symmetry_nbd_other 0.188 r_symmetry_nbd_refined 0.184 r_nbtor_refined 0.171 r_symmetry_xyhbond_nbd_refined 0.152 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.092 r_symmetry_nbtor_other 0.088 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2271 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing