4BVF

CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH THIOALKYLIMIDATE FORMED FROM THIO-ACETYL-LYSINE ACS2-PEPTIDE CRYSTALLIZED IN PRESENCE OF THE INHIBITOR EX-527


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.625% PEG 3350, 0.2 M LISO4, 0.1 M NA CITRATE PH 5.6
Crystal Properties
Matthews coefficientSolvent content
2.9458.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.5α = 90
b = 127.55β = 90
c = 76.34γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDCOLLIMATOR2012-01-28MSINGLE 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
12.733.799.80.1311.8511091-3
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)
12.72.7799.90.5634.9

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3GLT2.733.731053655599.780.170930.167810.23024RANDOM33.823
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]
0.82-0.65-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.832
r_dihedral_angle_3_deg17.392
r_dihedral_angle_4_deg16.88
r_dihedral_angle_1_deg6.076
r_mcangle_it3.971
r_scbond_it3.183
r_mcbond_it2.492
r_angle_refined_deg1.765
r_chiral_restr0.111
r_bond_refined_d0.013
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.832
r_dihedral_angle_3_deg17.392
r_dihedral_angle_4_deg16.88
r_dihedral_angle_1_deg6.076
r_mcangle_it3.971
r_scbond_it3.183
r_mcbond_it2.492
r_angle_refined_deg1.765
r_chiral_restr0.111
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_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 Atoms2227
Nucleic Acid Atoms
Solvent Atoms82
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing