4BV3

CRYSTAL STRUCTURE OF SIRT3 IN COMPLEX WITH THE INHIBITOR EX-527 AND NAD


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GLTPDB ENTRY 3GLT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.2 M (NH4)2SO4, 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.0339.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.94α = 90
b = 63.38β = 90
c = 66.35γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDCOLLIMATOR2011-09-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.1BESSY14.1

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
1245.899.30.1115.6617814-3
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)
122.0595.40.652.95.3

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3GLT245.831692289199.330.165440.163080.20942RANDOM20.044
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]
-0.790.240.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.43
r_dihedral_angle_4_deg16.623
r_dihedral_angle_3_deg14.162
r_dihedral_angle_1_deg6.333
r_mcangle_it2.413
r_scbond_it2.246
r_angle_refined_deg2.009
r_mcbond_it1.622
r_mcbond_other1.618
r_angle_other_deg0.975
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.43
r_dihedral_angle_4_deg16.623
r_dihedral_angle_3_deg14.162
r_dihedral_angle_1_deg6.333
r_mcangle_it2.413
r_scbond_it2.246
r_angle_refined_deg2.009
r_mcbond_it1.622
r_mcbond_other1.618
r_angle_other_deg0.975
r_chiral_restr0.113
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.001
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2123
Nucleic Acid Atoms
Solvent Atoms123
Heterogen Atoms116

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing