6AYQ

Crystal structure of Campylobacter jejuni 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with methylthio-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 DROP6.5295100 mM Bis-Tris pH 6.5, 28% (w/v) PEG MME 2000
Crystal Properties
Matthews coefficientSolvent content
2.141.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.13α = 90
b = 90.092β = 104.56
c = 67.826γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252016-12-06MSINGLE 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
11.4265.6599.80.9915.44.281192
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)
11.421.451000.7124.1

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 REPLACEMENTTHROUGHOUT4WKN1.4265.6577181397799.830.172330.171650.18533RANDOM18.686
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]
0.920.35-0.94-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.866
r_dihedral_angle_4_deg21.863
r_dihedral_angle_3_deg12.534
r_dihedral_angle_1_deg6.073
r_long_range_B_refined3.782
r_long_range_B_other3.782
r_scangle_other1.936
r_mcangle_it1.441
r_mcangle_other1.441
r_angle_refined_deg1.386
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.866
r_dihedral_angle_4_deg21.863
r_dihedral_angle_3_deg12.534
r_dihedral_angle_1_deg6.073
r_long_range_B_refined3.782
r_long_range_B_other3.782
r_scangle_other1.936
r_mcangle_it1.441
r_mcangle_other1.441
r_angle_refined_deg1.386
r_scbond_it1.199
r_scbond_other1.198
r_angle_other_deg0.887
r_mcbond_it0.864
r_mcbond_other0.862
r_chiral_restr0.159
r_bond_refined_d0.007
r_gen_planes_refined0.005
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 Atoms3486
Nucleic Acid Atoms
Solvent Atoms473
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing