8V2N | pdb_00008v2n

Human SIRT3 co-crystallized with ligands, including p53-AMC peptide and Carba-NAD


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4C7B 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION293.15SIRT3 (118-399) (10.3 mg/ml) was crystallized in complex with FDL (QPKKAC-7-amino-4-methylcoumarin) peptide (3 mM) and honokiol (1 mM) in 25% PEG 3350, 0.2 M Li2SO4 (or 0.2 M NaCl), and 0.1M HEPES, pH 7.5 as reservoir. Following formation of the ternary complex, crystals were soaked with carba-NAD (10 mM).
Crystal Properties
Matthews coefficientSolvent content
2.1337

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.339α = 90
b = 53.178β = 91.75
c = 68.539γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-06-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.979257ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.7442.0499.10.9937.44.225473
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.741.770.649

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.7442.0424207125999.060.243830.241860.240.281550.28RANDOM26.339
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]
-1.20.19-0.561.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.412
r_dihedral_angle_3_deg16.375
r_dihedral_angle_4_deg16.286
r_dihedral_angle_1_deg7.872
r_long_range_B_refined5.675
r_mcangle_it2.836
r_scbond_it2.546
r_mcbond_it1.988
r_angle_refined_deg0.806
r_chiral_restr0.066
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.412
r_dihedral_angle_3_deg16.375
r_dihedral_angle_4_deg16.286
r_dihedral_angle_1_deg7.872
r_long_range_B_refined5.675
r_mcangle_it2.836
r_scbond_it2.546
r_mcbond_it1.988
r_angle_refined_deg0.806
r_chiral_restr0.066
r_gen_planes_refined0.01
r_bond_refined_d0.008
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_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2070
Nucleic Acid Atoms
Solvent Atoms60
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata processing