3FQF

Staphylococcus aureus F98Y mutant dihydrofolate reductase complexed with NADPH and 2,4-diamino-5-[3-(3,4,5-trimethoxyphenyl)pent-1-ynyl]-6-methylpyrimidine (UCP115A)


X-RAY DIFFRACTION

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
2.7354.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.218α = 90
b = 79.218β = 90
c = 108.746γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77.2CCDADSC QUANTUM 3152008-04-19MSINGLE 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
11.7732.7289.40.0680.0681.411.1172143
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)
11.771.821000.1670.1671.111.41374

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)1.7732.72172141721494789.380.2090.2090.2070.245RANDOM14.909
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.007
r_dihedral_angle_4_deg19.949
r_dihedral_angle_3_deg15.308
r_dihedral_angle_1_deg6.546
r_angle_other_deg3.31
r_scangle_it2.328
r_scbond_it1.45
r_angle_refined_deg1.392
r_mcangle_it1.112
r_mcbond_it0.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.007
r_dihedral_angle_4_deg19.949
r_dihedral_angle_3_deg15.308
r_dihedral_angle_1_deg6.546
r_angle_other_deg3.31
r_scangle_it2.328
r_scbond_it1.45
r_angle_refined_deg1.392
r_mcangle_it1.112
r_mcbond_it0.64
r_nbtor_refined0.309
r_chiral_restr0.242
r_symmetry_vdw_refined0.2
r_nbd_refined0.195
r_nbd_other0.191
r_symmetry_hbond_refined0.173
r_xyhbond_nbd_refined0.137
r_symmetry_vdw_other0.096
r_nbtor_other0.095
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1274
Nucleic Acid Atoms
Solvent Atoms184
Heterogen Atoms74

Software

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