5DY4

Crystal structure of human Sirt2 in complex with a brominated 2nd generation SirReal inhibitor and NAD+


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4RMG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP727827 % PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.9658.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.303α = 90
b = 55.432β = 114.91
c = 96.176γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-10-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0SLSX06SA

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
11.7746.7898.20.09510.36.738622
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.771.8198.12.0516.9

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 REPLACEMENTTHROUGHOUT4RMG1.7746.7836691191397.90.176860.174940.21286RANDOM33.455
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]
-1.09-11.340.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.249
r_dihedral_angle_4_deg16.205
r_dihedral_angle_3_deg12.633
r_dihedral_angle_1_deg6.155
r_long_range_B_refined5.088
r_long_range_B_other5.027
r_scangle_other3.101
r_mcangle_it2.421
r_mcangle_other2.421
r_scbond_it1.897
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.249
r_dihedral_angle_4_deg16.205
r_dihedral_angle_3_deg12.633
r_dihedral_angle_1_deg6.155
r_long_range_B_refined5.088
r_long_range_B_other5.027
r_scangle_other3.101
r_mcangle_it2.421
r_mcangle_other2.421
r_scbond_it1.897
r_scbond_other1.896
r_angle_refined_deg1.646
r_mcbond_it1.484
r_mcbond_other1.484
r_angle_other_deg1.021
r_chiral_restr0.098
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.002
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 Atoms2391
Nucleic Acid Atoms
Solvent Atoms183
Heterogen Atoms75

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing