5V7A

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)acetic acid


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.22810.266 M MgCl2 28.5 %(w/v) PEG 6000 0.1 M sodium cacodylate, pH 6.2 Protein at 11.1 mg.mL-1 Co-crystallisation 1:1 (150:150 nL) reservoir:protein
Crystal Properties
Matthews coefficientSolvent content
2.5952.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.27α = 90
b = 84.83β = 109.23
c = 83.78γ = 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 MX10.95370Australian SynchrotronMX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.3561.7210013.57.426259

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 REPLACEMENTTHROUGHOUT1AJ22.3561.7224967128899.960.198170.195820.2433RANDOM35.815
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]
0.61.320.77-1.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.755
r_dihedral_angle_3_deg14.201
r_dihedral_angle_4_deg13.695
r_long_range_B_refined6.011
r_long_range_B_other6.01
r_dihedral_angle_1_deg5.789
r_scangle_other5.615
r_scbond_it4.374
r_scbond_other4.373
r_mcangle_it4.048
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.755
r_dihedral_angle_3_deg14.201
r_dihedral_angle_4_deg13.695
r_long_range_B_refined6.011
r_long_range_B_other6.01
r_dihedral_angle_1_deg5.789
r_scangle_other5.615
r_scbond_it4.374
r_scbond_other4.373
r_mcangle_it4.048
r_mcangle_other4.048
r_angle_other_deg3.722
r_mcbond_it3.041
r_mcbond_other3.039
r_angle_refined_deg1.433
r_chiral_restr0.075
r_bond_refined_d0.01
r_gen_planes_refined0.006
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 Atoms3955
Nucleic Acid Atoms
Solvent Atoms106
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing