6FKY

Crystal structure of zebrafish Sirtuin 5 in complex with 3-(benzylthio)succinyl-CPS1 peptide


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.1 M HEPES pH 7.4, 20% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.6353.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.134α = 90
b = 87.134β = 90
c = 316.677γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2MMIRRORS2016-05-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.918409BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)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
12.985099.80.3580.9949.815.515459
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.983.1699.12.10.5131.316

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 REPLACEMENTTHROUGHOUT4utv2.9848.511468677399.770.201630.197850.27485RANDOM67.667
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]
0.220.110.22-0.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.391
r_dihedral_angle_4_deg20.627
r_dihedral_angle_3_deg18.049
r_long_range_B_refined7.586
r_long_range_B_other7.583
r_dihedral_angle_1_deg6.543
r_scangle_other5.166
r_mcangle_it4.998
r_mcangle_other4.997
r_scbond_it3.182
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.391
r_dihedral_angle_4_deg20.627
r_dihedral_angle_3_deg18.049
r_long_range_B_refined7.586
r_long_range_B_other7.583
r_dihedral_angle_1_deg6.543
r_scangle_other5.166
r_mcangle_it4.998
r_mcangle_other4.997
r_scbond_it3.182
r_scbond_other3.182
r_mcbond_it3.015
r_mcbond_other3.015
r_angle_refined_deg1.872
r_angle_other_deg1.099
r_chiral_restr0.1
r_bond_refined_d0.014
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 Atoms4232
Nucleic Acid Atoms
Solvent Atoms55
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing