6DYV

Crystal structure of Helicobacter pylori 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with (3R,4S)-1-((4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl)-4-((pent-4-yn-1-ylthio)methyl)pyrrolidin-3-ol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4WKPPDB entry 4WKP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5295100 mM HEPES, pH 7.5, 20% w/v PEG8000
Crystal Properties
Matthews coefficientSolvent content
2.244.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.479α = 90
b = 73.479β = 90
c = 176.205γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HEKB mirrors2017-10-24MSINGLE 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
11.6288.198.70.99814.813.961452
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)
11.621.650.696

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 REPLACEMENTTHROUGHOUTPDB entry 4WKP1.6267.8258317305598.570.168030.166720.1932RANDOM21.099
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]
0.450.45-0.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.816
r_dihedral_angle_4_deg15.931
r_dihedral_angle_3_deg13.036
r_dihedral_angle_1_deg5.607
r_long_range_B_refined4.785
r_long_range_B_other4.784
r_scangle_other2.98
r_scbond_it1.915
r_scbond_other1.915
r_mcangle_it1.811
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.816
r_dihedral_angle_4_deg15.931
r_dihedral_angle_3_deg13.036
r_dihedral_angle_1_deg5.607
r_long_range_B_refined4.785
r_long_range_B_other4.784
r_scangle_other2.98
r_scbond_it1.915
r_scbond_other1.915
r_mcangle_it1.811
r_mcangle_other1.811
r_angle_refined_deg1.553
r_mcbond_it1.173
r_mcbond_other1.172
r_angle_other_deg0.955
r_chiral_restr0.088
r_bond_refined_d0.01
r_gen_planes_refined0.006
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 Atoms3525
Nucleic Acid Atoms
Solvent Atoms481
Heterogen Atoms84

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing