3FQV

Staphylococcus aureus F98Y mutant dihydrofolate reductase complexed with NADPH and 2,4-diamino-5-[3-(3-methoxy-4-phenylphenyl)but-1-ynyl]-6-methylpyrimidine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherSa F98Y DHFR bound to Folate and NADPH (Dale et al., J.Mol.Biol. 1997, structure not deposited in the PDB)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.527715% PEG 10000, 150mM Sodium acetate, 100mM MES pH 6.5, 5% Butyrlactone, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.754.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.897α = 90
b = 78.897β = 90
c = 108.189γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77.2CCDADSC QUANTUM 3152008-06-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.080900NSLSX29A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.8537.0699.20.0470.0472.710165973
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.9299.50.0960.0960.98.11203

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONDIFFERENCE FOURIERTHROUGHOUTSa F98Y DHFR bound to Folate and NADPH (Dale et al., J.Mol.Biol. 1997, structure not deposited in the PDB)1.8537.06165971659788899.20.2250.2250.2230.266RANDOM18.144
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]
-0.01-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.856
r_dihedral_angle_3_deg14.161
r_dihedral_angle_4_deg11.555
r_dihedral_angle_1_deg6.712
r_scangle_it1.732
r_angle_refined_deg1.417
r_scbond_it1.078
r_mcangle_it1.012
r_mcbond_it0.58
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.856
r_dihedral_angle_3_deg14.161
r_dihedral_angle_4_deg11.555
r_dihedral_angle_1_deg6.712
r_scangle_it1.732
r_angle_refined_deg1.417
r_scbond_it1.078
r_mcangle_it1.012
r_mcbond_it0.58
r_nbtor_refined0.308
r_symmetry_vdw_refined0.279
r_symmetry_hbond_refined0.231
r_nbd_refined0.192
r_xyhbond_nbd_refined0.144
r_chiral_restr0.094
r_bond_refined_d0.007
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1274
Nucleic Acid Atoms
Solvent Atoms147
Heterogen Atoms75

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
Cootmodel building
CCP4phasing