8I2B

Human SIRT6 in complex with inhibitor 7702


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6HOY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2910.1M Bis-tris pH 5.7, 1.6 M (NH4)2SO4, 10% PEG400
Crystal Properties
Matthews coefficientSolvent content
2.7655.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.318α = 90
b = 91.318β = 90
c = 143.674γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 S 16M2022-10-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL10U20.9792SSRFBL10U2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.240.9799.90.9915.3519.1734506
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2790.965

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.240.9732687173599.960.194420.192230.23751RANDOM47.79
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]
0.020.02-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.109
r_dihedral_angle_4_deg17.847
r_dihedral_angle_3_deg15.455
r_long_range_B_other11.043
r_long_range_B_refined11.037
r_scangle_other7.364
r_dihedral_angle_1_deg7.04
r_mcangle_it5.845
r_mcangle_other5.845
r_scbond_it5.215
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.109
r_dihedral_angle_4_deg17.847
r_dihedral_angle_3_deg15.455
r_long_range_B_other11.043
r_long_range_B_refined11.037
r_scangle_other7.364
r_dihedral_angle_1_deg7.04
r_mcangle_it5.845
r_mcangle_other5.845
r_scbond_it5.215
r_scbond_other5.18
r_mcbond_it4.519
r_mcbond_other4.517
r_angle_refined_deg1.598
r_angle_other_deg1.292
r_chiral_restr0.079
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms4392
Nucleic Acid Atoms
Solvent Atoms77
Heterogen Atoms202

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing