3K2H

Co-crystal structure of dihydrofolate reductase/thymidylate synthase from Babesia bovis with dUMP, Pemetrexed and NADP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3I3R 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9.528911.3 mg/mL BaboA.01191.a, 2 mM dUMP, 2 mM Pemetrexed, NADP carried through from protein purification so it could be NADP or NADPH; soak of apo crystals grown in 20% PEG 8000, 0.1 M CHES pH 9.5; crystal tracking ID 204850f1, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.5652.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.144α = 119.69
b = 83.196β = 90.85
c = 83.378γ = 101.71
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2009-09-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.5418

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
12.25098.50.09615.4458064
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)
12.22.2482.60.2863.162.72401

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 REPLACEMENTTHROUGHOUT3i3r2.235.257443291797.030.1920.190.239RANDOM16.674
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]
1.40.60.21-0.060.78-0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.686
r_dihedral_angle_4_deg21.604
r_dihedral_angle_3_deg14.171
r_dihedral_angle_1_deg6.556
r_scangle_it2.851
r_scbond_it1.933
r_angle_refined_deg1.507
r_mcangle_it1.17
r_mcbond_it0.654
r_chiral_restr0.109
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.686
r_dihedral_angle_4_deg21.604
r_dihedral_angle_3_deg14.171
r_dihedral_angle_1_deg6.556
r_scangle_it2.851
r_scbond_it1.933
r_angle_refined_deg1.507
r_mcangle_it1.17
r_mcbond_it0.654
r_chiral_restr0.109
r_bond_refined_d0.014
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8001
Nucleic Acid Atoms
Solvent Atoms727
Heterogen Atoms280

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling