3LG4

Staphylococcus aureus V31Y, F92I mutant dihydrofolate reductase complexed with NADPH and 5-[(3S)-3-(5-methoxy-2',6'-dimethylbiphenyl-3-yl)but-1-yn-1-yl]-6-methylpyrimidine-2,4-diamine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3F0QPDB ENTRY 3F0Q

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.527715% (w/v) PEG 10000, 150 mM sodium acetate, 100 mM MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
359.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.752α = 90
b = 88.752β = 90
c = 103.167γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77.2CCDADSC QUANTUM 3152009-08-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X250.99700NSLSX25

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
13.1542.8491.20.0610.06114.55803868393387.41
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)
13.153.23199.70.3790.3792.965.4558

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3F0Q3.1542.846251625131885.080.26140.26140.260.2924RANDOM88.7044
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_deg36.822
r_dihedral_angle_4_deg22.334
r_dihedral_angle_3_deg17.782
r_dihedral_angle_1_deg5.651
r_angle_refined_deg1.219
r_scangle_it0.994
r_mcangle_it0.558
r_scbond_it0.545
r_nbtor_refined0.309
r_mcbond_it0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.822
r_dihedral_angle_4_deg22.334
r_dihedral_angle_3_deg17.782
r_dihedral_angle_1_deg5.651
r_angle_refined_deg1.219
r_scangle_it0.994
r_mcangle_it0.558
r_scbond_it0.545
r_nbtor_refined0.309
r_mcbond_it0.306
r_symmetry_vdw_refined0.223
r_nbd_refined0.191
r_xyhbond_nbd_refined0.162
r_symmetry_hbond_refined0.114
r_chiral_restr0.075
r_bond_refined_d0.007
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2548
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms154

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction
SCALEPACKdata scaling
Cootmodel building