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Human SIRT2 in Complex with RW-80
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9S44
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293.15 0.1 M sodium acetate
17 % (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.15 42.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.9 α = 90 b = 73.71 β = 94.78 c = 55.86 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 EIGER2 S 16M 2025-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.0596 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.45 30 96.7 0.079 9.47 3.5 49669
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.55 95 0.788 1.99 3.5
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.45 30 47182 2483 96.7 0.15765 0.15608 0.1677 0.18722 0.1909 RANDOM 18.596
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] 0.34 0.05 0.16 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.108 r_dihedral_angle_4_deg 20.697 r_dihedral_angle_3_deg 11.379 r_dihedral_angle_1_deg 6.476 r_long_range_B_refined 2.323 r_long_range_B_other 2.323 r_scangle_other 1.292 r_angle_other_deg 1.204 r_angle_refined_deg 1.187 r_mcangle_it 1.149
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.108 r_dihedral_angle_4_deg 20.697 r_dihedral_angle_3_deg 11.379 r_dihedral_angle_1_deg 6.476 r_long_range_B_refined 2.323 r_long_range_B_other 2.323 r_scangle_other 1.292 r_angle_other_deg 1.204 r_angle_refined_deg 1.187 r_mcangle_it 1.149 r_mcangle_other 1.149 r_scbond_it 0.998 r_scbond_other 0.998 r_mcbond_it 0.823 r_mcbond_other 0.817 r_rigid_bond_restr 0.458 r_chiral_restr 0.057 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2309 Nucleic Acid Atoms Solvent Atoms 241 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing