6DYY

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-(((3-(1-butyl-1H-1,2,3-triazol-4-yl)propyl)thio)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 DROP295200 mM calcium chloride, 20% w/v PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.244.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.564α = 90
b = 74.028β = 90
c = 176.887γ = 90
Symmetry
Space GroupP 21 21 21

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
11.6188.441000.9911.47.4123910
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)
11.611.640.82.1

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 REPLACEMENTTHROUGHOUTPDB entry 4WKP1.6188.44117541626599.950.180480.179270.20328RANDOM23.601
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]
-0.411.88-1.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.434
r_dihedral_angle_4_deg16.417
r_dihedral_angle_3_deg12.969
r_dihedral_angle_1_deg5.731
r_long_range_B_refined4.887
r_long_range_B_other4.887
r_scangle_other3.261
r_scbond_it2.053
r_scbond_other2.053
r_mcangle_it2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.434
r_dihedral_angle_4_deg16.417
r_dihedral_angle_3_deg12.969
r_dihedral_angle_1_deg5.731
r_long_range_B_refined4.887
r_long_range_B_other4.887
r_scangle_other3.261
r_scbond_it2.053
r_scbond_other2.053
r_mcangle_it2
r_mcangle_other2
r_angle_refined_deg1.49
r_mcbond_it1.303
r_mcbond_other1.303
r_angle_other_deg0.935
r_chiral_restr0.085
r_bond_refined_d0.009
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 Atoms7042
Nucleic Acid Atoms
Solvent Atoms894
Heterogen Atoms154

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing