6AYM

Crystal structure of Campylobacter jejuni 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN)


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 MES pH 6.5, 600 mM Sodium Chloride, 20% (w/v) PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.347.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.408α = 90
b = 84.62β = 90
c = 124.881γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252017-06-14MSINGLE 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
11.2570.0598.30.9914.87.3134158
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)
11.251.2796.50.651.97.4

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 REPLACEMENTTHROUGHOUT4WKN1.2570.05127260680798.190.190410.189590.20532RANDOM15.327
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]
-0.480.320.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.53
r_dihedral_angle_4_deg17.915
r_dihedral_angle_3_deg12.972
r_dihedral_angle_1_deg6.07
r_long_range_B_refined4.755
r_long_range_B_other4.755
r_scangle_other1.879
r_mcangle_it1.426
r_mcangle_other1.425
r_angle_refined_deg1.335
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.53
r_dihedral_angle_4_deg17.915
r_dihedral_angle_3_deg12.972
r_dihedral_angle_1_deg6.07
r_long_range_B_refined4.755
r_long_range_B_other4.755
r_scangle_other1.879
r_mcangle_it1.426
r_mcangle_other1.425
r_angle_refined_deg1.335
r_scbond_it1.162
r_scbond_other1.161
r_angle_other_deg0.935
r_mcbond_it0.83
r_mcbond_other0.829
r_chiral_restr0.139
r_bond_refined_d0.008
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 Atoms3521
Nucleic Acid Atoms
Solvent Atoms601
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing