3DAT

Crystal structure of the ternary MTX NADPH complex of Bacillus anthracis dihydrofolate reductase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QK8PDB entry 2QK8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52770.1 M Bis-Tris pH 5.5, 0.2 M CaCl2, 20% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.7354.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.9α = 90
b = 43.156β = 119.31
c = 67.87γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmMirrors2008-03-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-ID-B0.90000APS14-ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.12093.80.1318.63.11021611
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.1773.30.28631.9823

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 2QK82.315.31118332817040491.920.2390.2370.277RANDOM44.502
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]
-0.03-0.210.14-0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.816
r_dihedral_angle_3_deg21.993
r_dihedral_angle_4_deg17.853
r_dihedral_angle_1_deg8.102
r_scangle_it2.87
r_angle_refined_deg1.892
r_scbond_it1.856
r_mcangle_it1.234
r_mcbond_it0.759
r_nbtor_refined0.323
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.816
r_dihedral_angle_3_deg21.993
r_dihedral_angle_4_deg17.853
r_dihedral_angle_1_deg8.102
r_scangle_it2.87
r_angle_refined_deg1.892
r_scbond_it1.856
r_mcangle_it1.234
r_mcbond_it0.759
r_nbtor_refined0.323
r_nbd_refined0.24
r_symmetry_hbond_refined0.201
r_xyhbond_nbd_refined0.178
r_symmetry_vdw_refined0.165
r_chiral_restr0.126
r_bond_refined_d0.017
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1280
Nucleic Acid Atoms
Solvent Atoms34
Heterogen Atoms81

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
BioCARSdata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing