6QCH

Human Sirt6 in complex with ADP-ribose and the activator cyanidin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5MF6 

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
2.6353.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.387α = 90
b = 91.387β = 90
c = 143.806γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-07-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.918BESSY14.1

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
12.147.9499.90.160.9981111.3397711.347.58
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)
12.12.2299.51.840.6341.311.3

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 REPLACEMENTTHROUGHOUT5MF62.145.6937769200199.90.165170.163280.19964RANDOM50.493
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]
-20.23-20.2340.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.865
r_dihedral_angle_4_deg20.735
r_dihedral_angle_3_deg15.81
r_long_range_B_refined11.226
r_long_range_B_other11.225
r_scangle_other8.388
r_dihedral_angle_1_deg7.46
r_mcangle_it6.545
r_mcangle_other6.544
r_scbond_it6.374
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.865
r_dihedral_angle_4_deg20.735
r_dihedral_angle_3_deg15.81
r_long_range_B_refined11.226
r_long_range_B_other11.225
r_scangle_other8.388
r_dihedral_angle_1_deg7.46
r_mcangle_it6.545
r_mcangle_other6.544
r_scbond_it6.374
r_scbond_other6.373
r_mcbond_other5.498
r_mcbond_it5.497
r_angle_other_deg2.356
r_angle_refined_deg1.95
r_chiral_restr0.094
r_bond_other_d0.034
r_gen_planes_other0.013
r_bond_refined_d0.012
r_gen_planes_refined0.011
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 Atoms4336
Nucleic Acid Atoms
Solvent Atoms117
Heterogen Atoms182

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing