6QCJ

Human Sirt6 in complex with ADP-ribose and the inhibitor catechin gallate


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
2.6753.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.917α = 90
b = 91.917β = 90
c = 144.368γ = 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
12.0148.1298.90.160.9969.710.1450891.338.92
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)
12.012.1496.21.90.711.38.5

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 REPLACEMENTTHROUGHOUT5MF62.0145.9642989209998.880.164740.163110.19853RANDOM38.796
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]
-22.25-22.2544.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.146
r_dihedral_angle_4_deg18.56
r_dihedral_angle_3_deg15.69
r_long_range_B_other9.11
r_long_range_B_refined9.107
r_dihedral_angle_1_deg8.312
r_scangle_other7.027
r_mcangle_it6.157
r_mcangle_other6.156
r_scbond_it5.476
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.146
r_dihedral_angle_4_deg18.56
r_dihedral_angle_3_deg15.69
r_long_range_B_other9.11
r_long_range_B_refined9.107
r_dihedral_angle_1_deg8.312
r_scangle_other7.027
r_mcangle_it6.157
r_mcangle_other6.156
r_scbond_it5.476
r_scbond_other5.475
r_mcbond_other4.888
r_mcbond_it4.887
r_angle_refined_deg2.281
r_angle_other_deg1.427
r_chiral_restr0.117
r_bond_refined_d0.016
r_gen_planes_refined0.013
r_bond_other_d0.003
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 Atoms4350
Nucleic Acid Atoms
Solvent Atoms166
Heterogen Atoms177

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing