8CNO

Improved complex structure of human Sirtuin 6 with its inhibitor cis-resveratrol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3K35 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.72931.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
Crystal Properties
Matthews coefficientSolvent content
2.6152.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.276α = 90
b = 91.276β = 90
c = 143.23γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-06-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.9184BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)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
11.7547.7499.90.120.99912.910.26798835.441
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.8699.52.110.4211.18

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 REPLACEMENTTHROUGHOUT1.7545.6465918206999.90.167250.16660.18761RANDOM33.955
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]
-9.14-9.1418.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.569
r_dihedral_angle_4_deg17.942
r_dihedral_angle_3_deg14.395
r_dihedral_angle_1_deg6.833
r_long_range_B_refined6.58
r_long_range_B_other6.549
r_scangle_other4.807
r_mcangle_other3.931
r_mcangle_it3.93
r_scbond_it3.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.569
r_dihedral_angle_4_deg17.942
r_dihedral_angle_3_deg14.395
r_dihedral_angle_1_deg6.833
r_long_range_B_refined6.58
r_long_range_B_other6.549
r_scangle_other4.807
r_mcangle_other3.931
r_mcangle_it3.93
r_scbond_it3.38
r_scbond_other3.343
r_mcbond_it2.968
r_mcbond_other2.967
r_angle_other_deg2.294
r_angle_refined_deg1.649
r_chiral_restr0.08
r_bond_other_d0.034
r_gen_planes_other0.018
r_bond_refined_d0.01
r_gen_planes_refined0.01
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 Atoms4364
Nucleic Acid Atoms
Solvent Atoms172
Heterogen Atoms197

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing