4O8Z

Crystal structure of human SIRT3 in complex with compound (2-butylbenzofuran-3-yl)(4-(2-(diethylamino)ethoxy)-3,5-diiodophenyl)methanone


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GLS 

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.6353.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.317α = 90
b = 116.317β = 90
c = 45.655γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray2013-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.979220SSRFBL17U

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
12100.730.09415.1624073
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)
122.050.4274.26

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 REPLACEMENTTHROUGHOUT3GLS2100.7322590121698.570.169280.167370.20373RANDOM32.239
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]
0.080.040.08-0.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.313
r_dihedral_angle_4_deg17.17
r_long_range_B_other15.697
r_long_range_B_refined15.584
r_dihedral_angle_3_deg14.089
r_scangle_other8.411
r_dihedral_angle_1_deg6.284
r_scbond_other5.665
r_mcangle_it4.034
r_scbond_it4.034
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.313
r_dihedral_angle_4_deg17.17
r_long_range_B_other15.697
r_long_range_B_refined15.584
r_dihedral_angle_3_deg14.089
r_scangle_other8.411
r_dihedral_angle_1_deg6.284
r_scbond_other5.665
r_mcangle_it4.034
r_scbond_it4.034
r_mcangle_other4.031
r_mcbond_it2.901
r_mcbond_other2.901
r_angle_refined_deg1.943
r_angle_other_deg1.048
r_chiral_restr0.118
r_bond_refined_d0.018
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 Atoms2133
Nucleic Acid Atoms
Solvent Atoms217
Heterogen Atoms32

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling