5MF6

Human Sirt6 in complex with activator UBCS039


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, Bis-Tris buffer pH 5.7
Crystal Properties
Matthews coefficientSolvent content
2.5952.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.3α = 90
b = 91.3β = 90
c = 144.317γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-06-28MSINGLE 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)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
11.8745.6599.80.1412.1410.3561181.93
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.871.9899.11.3210.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT3K351.8745.6553308281099.820.191410.189880.21957RANDOM32.836
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]
-8.6-8.617.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.336
r_dihedral_angle_4_deg17.744
r_dihedral_angle_3_deg15.616
r_long_range_B_refined7.601
r_long_range_B_other7.6
r_dihedral_angle_1_deg6.54
r_scangle_other6.111
r_mcangle_it4.363
r_mcangle_other4.363
r_scbond_it4.358
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.336
r_dihedral_angle_4_deg17.744
r_dihedral_angle_3_deg15.616
r_long_range_B_refined7.601
r_long_range_B_other7.6
r_dihedral_angle_1_deg6.54
r_scangle_other6.111
r_mcangle_it4.363
r_mcangle_other4.363
r_scbond_it4.358
r_scbond_other4.357
r_mcbond_it3.408
r_mcbond_other3.4
r_angle_refined_deg2.324
r_angle_other_deg1.301
r_chiral_restr0.141
r_bond_refined_d0.022
r_gen_planes_refined0.012
r_bond_other_d0.003
r_gen_planes_other0.002
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 Atoms4337
Nucleic Acid Atoms
Solvent Atoms174
Heterogen Atoms174

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing