5OJN

Sirtuin 4 from Xenopus tropicalis in complex with thioacetyl-ADP-ribose


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82770.5 M Na/K-tartrate 0.5% PEG5000MME 0.1 M Tris
Crystal Properties
Matthews coefficientSolvent content
2.244.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.97α = 90
b = 74.88β = 90
c = 109.55γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MSagitally bended Si111-crystal2015-09-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.976250BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.82099.70.0550.99918.36.826585
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8599.91.040.7042.17.1

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 REPLACEMENTTHROUGHOUT5OJ71.819.7425255133099.740.157870.155280.20883RANDOM38.417
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]
-0.621.27-0.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.154
r_dihedral_angle_4_deg14.717
r_dihedral_angle_3_deg14.372
r_long_range_B_refined7.856
r_long_range_B_other7.854
r_scangle_other6.428
r_dihedral_angle_1_deg6.371
r_scbond_other4.313
r_scbond_it4.309
r_mcangle_it3.728
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.154
r_dihedral_angle_4_deg14.717
r_dihedral_angle_3_deg14.372
r_long_range_B_refined7.856
r_long_range_B_other7.854
r_scangle_other6.428
r_dihedral_angle_1_deg6.371
r_scbond_other4.313
r_scbond_it4.309
r_mcangle_it3.728
r_mcangle_other3.727
r_mcbond_other2.753
r_mcbond_it2.752
r_angle_refined_deg2.438
r_angle_other_deg1.26
r_chiral_restr0.162
r_bond_refined_d0.029
r_gen_planes_refined0.014
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 Atoms2153
Nucleic Acid Atoms
Solvent Atoms179
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing