6AYT

Crystal structure of Campylobacter jejuni 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with pyrazinylthio-DADMe-Immucillin-A


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5295100 mM HEPES pH 7.5, 200 mM Magnesium Chloride, 25% (w/v) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.140.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.078α = 90
b = 90.983β = 111.44
c = 72.451γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252017-03-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.97931APS31-ID

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
11.8567.4499.90.9910.27.473146
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)
11.851.891000.891.97.5

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 REPLACEMENTTHROUGHOUT4WKN1.8567.4469342370399.720.220530.21920.24494RANDOM26.36
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]
1.65-1.08-0.16-0.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.174
r_dihedral_angle_4_deg27.766
r_dihedral_angle_3_deg12.991
r_dihedral_angle_1_deg6.419
r_long_range_B_refined3.721
r_long_range_B_other3.72
r_scangle_other2.109
r_mcangle_it1.887
r_mcangle_other1.887
r_angle_refined_deg1.281
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.174
r_dihedral_angle_4_deg27.766
r_dihedral_angle_3_deg12.991
r_dihedral_angle_1_deg6.419
r_long_range_B_refined3.721
r_long_range_B_other3.72
r_scangle_other2.109
r_mcangle_it1.887
r_mcangle_other1.887
r_angle_refined_deg1.281
r_scbond_it1.238
r_scbond_other1.238
r_mcbond_it1.097
r_mcbond_other1.097
r_angle_other_deg0.879
r_chiral_restr0.071
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.002
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 Atoms7056
Nucleic Acid Atoms
Solvent Atoms509
Heterogen Atoms112

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing