5V79

E. coli dihydropteroate synthase complexed with an 8-mercaptoguanine derivative: 2-((2-amino-9-methyl-6-oxo-6,9-dihydro-1H-purin-8-yl)thio)-N-phenylacetamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AJ2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.82810.248 M magnesium nitrate 20.3 %(w/v) PEG 8000 0.1 M tris chloride, pH 8.8 Protein at 11.1 mg.mL-1 1:1 (150:150 nL) reservoir:protein Ligand soaked into crystal (~4 h, ~2 mM)
Crystal Properties
Matthews coefficientSolvent content
2.6253

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.364α = 90
b = 85.621β = 109.67
c = 83.865γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102017-03-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.9537Australian SynchrotronMX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
12.2546.398.40.190.0820.99511.36.429678
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.252.3299.51.1120.4470.8652.87.32

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 REPLACEMENTTHROUGHOUT1AJ22.2546.328201146598.090.198460.196690.23162RANDOM39.806
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]
1.671.580.23-2.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.827
r_dihedral_angle_3_deg13.148
r_dihedral_angle_4_deg13.006
r_long_range_B_refined5.752
r_long_range_B_other5.751
r_dihedral_angle_1_deg5.512
r_scangle_other3.981
r_angle_other_deg3.724
r_mcangle_it3.589
r_mcangle_other3.589
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.827
r_dihedral_angle_3_deg13.148
r_dihedral_angle_4_deg13.006
r_long_range_B_refined5.752
r_long_range_B_other5.751
r_dihedral_angle_1_deg5.512
r_scangle_other3.981
r_angle_other_deg3.724
r_mcangle_it3.589
r_mcangle_other3.589
r_scbond_it2.388
r_scbond_other2.388
r_mcbond_it2.196
r_mcbond_other2.19
r_angle_refined_deg1.411
r_chiral_restr0.076
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_gen_planes_other0.005
r_bond_other_d
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 Atoms3983
Nucleic Acid Atoms
Solvent Atoms117
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing