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Human SIRT6 in complex with EGCG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZG6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.7 291.15 1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
Crystal Properties Matthews coefficient Solvent content 2.76 55.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.2 α = 90 b = 91.2 β = 90 c = 143.71 γ = 120
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 2024-03-16 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) 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 2.4 45.6 100 0.164 13.9 19.9 26481
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 2.4 2.49 1.124
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 2.5 45.6 22302 1141 99.97 0.15029 0.14756 0.1542 0.20524 0.2051 RANDOM 53.908
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] 0.04 0.04 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.399 r_dihedral_angle_4_deg 20.172 r_dihedral_angle_3_deg 17.986 r_long_range_B_refined 10.315 r_long_range_B_other 10.314 r_scangle_other 7.236 r_dihedral_angle_1_deg 7.09 r_mcangle_it 6.423 r_mcangle_other 6.422 r_scbond_it 5.141
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.399 r_dihedral_angle_4_deg 20.172 r_dihedral_angle_3_deg 17.986 r_long_range_B_refined 10.315 r_long_range_B_other 10.314 r_scangle_other 7.236 r_dihedral_angle_1_deg 7.09 r_mcangle_it 6.423 r_mcangle_other 6.422 r_scbond_it 5.141 r_scbond_other 5.124 r_mcbond_other 4.718 r_mcbond_it 4.717 r_angle_refined_deg 1.672 r_angle_other_deg 1.296 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4387 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 107
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing