5Y2F

Human SIRT6 in complex with allosteric activator MDL-801


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5291.150.2 M (NH4)2SO4, 0.1 M Mes pH 6.5, 20% W/v PEG 8000
Crystal Properties
Matthews coefficientSolvent content
4.9772.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 162.422α = 90
b = 162.422β = 90
c = 162.422γ = 90
Symmetry
Space GroupP 41 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002016-08-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97857APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.53114.8598.70.13730.842.724828
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.532.6610041.9

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 DIFFRACTIONTHROUGHOUT2.53114.8523520126198.710.177240.175050.21664RANDOM69.863
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.347
r_dihedral_angle_4_deg18.681
r_dihedral_angle_3_deg14.924
r_long_range_B_other13.005
r_long_range_B_refined12.941
r_scangle_other8.344
r_mcangle_it6.958
r_mcangle_other6.958
r_dihedral_angle_1_deg5.846
r_scbond_it5.217
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.347
r_dihedral_angle_4_deg18.681
r_dihedral_angle_3_deg14.924
r_long_range_B_other13.005
r_long_range_B_refined12.941
r_scangle_other8.344
r_mcangle_it6.958
r_mcangle_other6.958
r_dihedral_angle_1_deg5.846
r_scbond_it5.217
r_scbond_other5.212
r_mcbond_it4.401
r_mcbond_other4.401
r_angle_refined_deg1.576
r_angle_other_deg0.99
r_chiral_restr0.081
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.002
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 Atoms2368
Nucleic Acid Atoms
Solvent Atoms132
Heterogen Atoms158

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data processing
Aimlessdata scaling
PHASERphasing