6EO0

Zebrafish Sirt5 in complex with stalled peptidylimidate and bicyclic intermediate of inhibitory compound 29


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529320% PEG8000, 0.2 M MgCl2, 0.1 M Tris/HCl pH 8.5, 0.1 M glycine
Crystal Properties
Matthews coefficientSolvent content
2.1141.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.93α = 90
b = 113.59β = 103.24
c = 72.31γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M-F2016-11-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA0.918400SLSX06DA

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
12.45096.20.2520.9896.13.838453
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)
12.42.597.31.7020.5170.93.8

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 REPLACEMENTTHROUGHOUT4UTV2.448.4136530192396.260.255310.252630.30492RANDOM52.227
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]
0.831.44-1.630.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.805
r_dihedral_angle_3_deg18.062
r_dihedral_angle_4_deg16.815
r_dihedral_angle_1_deg6.542
r_long_range_B_refined6.122
r_long_range_B_other6.115
r_mcangle_it3.328
r_mcangle_other3.328
r_scangle_other3.078
r_mcbond_it2.032
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.805
r_dihedral_angle_3_deg18.062
r_dihedral_angle_4_deg16.815
r_dihedral_angle_1_deg6.542
r_long_range_B_refined6.122
r_long_range_B_other6.115
r_mcangle_it3.328
r_mcangle_other3.328
r_scangle_other3.078
r_mcbond_it2.032
r_mcbond_other2.032
r_scbond_it1.983
r_scbond_other1.983
r_angle_refined_deg1.967
r_angle_other_deg1.3
r_chiral_restr0.1
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_bond_other_d0.005
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 Atoms8541
Nucleic Acid Atoms
Solvent Atoms176
Heterogen Atoms420

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing