6ENX

Zebrafish Sirt5 in complex with stalled bicyclic intermediate of inhibitory compound 10


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
2.3647.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.47α = 90
b = 38.25β = 122.51
c = 75.55γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M-F2016-12-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.000030SLSX06DA

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
11.955099.10.2130.9896.84.120704
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)
11.95299.21.5650.4631.14.1

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 REPLACEMENTTHROUGHOUT4UTV1.9549.1119704103799.620.197060.194670.24169RANDOM26.588
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]
-1.180.210.120.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.337
r_dihedral_angle_4_deg18.355
r_dihedral_angle_3_deg16.058
r_dihedral_angle_1_deg6.2
r_long_range_B_refined5.529
r_long_range_B_other5.528
r_scangle_other4.183
r_mcangle_it2.731
r_mcangle_other2.73
r_scbond_other2.693
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.337
r_dihedral_angle_4_deg18.355
r_dihedral_angle_3_deg16.058
r_dihedral_angle_1_deg6.2
r_long_range_B_refined5.529
r_long_range_B_other5.528
r_scangle_other4.183
r_mcangle_it2.731
r_mcangle_other2.73
r_scbond_other2.693
r_scbond_it2.691
r_angle_refined_deg1.971
r_mcbond_it1.91
r_mcbond_other1.91
r_angle_other_deg1.162
r_chiral_restr0.115
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.004
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2072
Nucleic Acid Atoms
Solvent Atoms173
Heterogen Atoms85

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing