6QCN

Human Sirt2 in complex with ADP-ribose and the inhibitor quercetin


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.829314% PEG 10,000, 0.1M ammonium acetate pH 5.8
Crystal Properties
Matthews coefficientSolvent content
2.6653.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.214α = 90
b = 78.302β = 90
c = 114.528γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-06-13MSINGLE 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
12.2346.2299.50.280.9764.47.4345740.752.37
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)
12.232.3797.11.90.2827.4

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 REPLACEMENTTHROUGHOUT5MAR2.2346.2232823174999.370.210530.209260.23405RANDOM49.105
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]
16.17-9.27-6.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.076
r_dihedral_angle_4_deg20.33
r_dihedral_angle_3_deg17.841
r_long_range_B_other10.472
r_long_range_B_refined10.468
r_dihedral_angle_1_deg9.142
r_mcangle_it8.5
r_mcangle_other8.499
r_scangle_other8.261
r_mcbond_it6.735
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.076
r_dihedral_angle_4_deg20.33
r_dihedral_angle_3_deg17.841
r_long_range_B_other10.472
r_long_range_B_refined10.468
r_dihedral_angle_1_deg9.142
r_mcangle_it8.5
r_mcangle_other8.499
r_scangle_other8.261
r_mcbond_it6.735
r_mcbond_other6.735
r_scbond_it6.708
r_scbond_other6.706
r_angle_refined_deg2.097
r_angle_other_deg1.328
r_chiral_restr0.1
r_bond_refined_d0.013
r_gen_planes_refined0.011
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 Atoms4735
Nucleic Acid Atoms
Solvent Atoms28
Heterogen Atoms96

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing