3H2O

Structural Studies of Pterin-Based Inhibitors of Dihydropteroate Synthase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1TX0PDB entry 1TX0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9291LITHIUM SULFATE, propane, Bis-Tris, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.8556.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.292α = 90
b = 99.292β = 90
c = 263.051γ = 120
Symmetry
Space GroupP 62 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2008-11-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (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
12.6148.7893.90.06638.211.922826
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.612.69620.167.17.21451

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 1TX02.748.7821380108497.280.273230.271280.31097RANDOM49.878
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]
6.563.286.56-9.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.755
r_dihedral_angle_3_deg21.095
r_dihedral_angle_4_deg17.598
r_dihedral_angle_1_deg7.971
r_scangle_it3.259
r_angle_refined_deg2.127
r_scbond_it2.103
r_mcangle_it1.303
r_mcbond_it0.754
r_nbtor_refined0.333
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.755
r_dihedral_angle_3_deg21.095
r_dihedral_angle_4_deg17.598
r_dihedral_angle_1_deg7.971
r_scangle_it3.259
r_angle_refined_deg2.127
r_scbond_it2.103
r_mcangle_it1.303
r_mcbond_it0.754
r_nbtor_refined0.333
r_nbd_refined0.28
r_symmetry_hbond_refined0.251
r_symmetry_vdw_refined0.238
r_xyhbond_nbd_refined0.195
r_chiral_restr0.136
r_bond_refined_d0.022
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3996
Nucleic Acid Atoms
Solvent Atoms5
Heterogen Atoms68

Software

Software
Software NamePurpose
SERGUIdata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling