3SGY

Staphylococcus aureus Dihydrofolate Reductase complexed with NADPH and 6-ETHYL-5-[(3S)-3-[3-METHOXY-5-(PYRIDIN-4-YL)PHENYL]BUT-1-YN-1-YL]PYRIMIDINE-2,4-DIAMINE (UCP1006)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherSa DHFR bound to Folate and NADPH (Dale et al. 1997)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.527715 % PEG 10000, 150 mM sodium acetate, 100 mM MES pH 6.5, 5 % butyrlactone, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4850.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.826α = 90
b = 78.826β = 90
c = 107.277γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77.2CCDADSC QUANTUM 3152010-05-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X251.1000NSLSX25

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
12.59842.1897.30.0820.08231.15.711695113793351.704
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)
12.5982.6498.80.2910.2915.55.7544

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 REPLACEMENTTHROUGHOUTSa DHFR bound to Folate and NADPH (Dale et al. 1997)2.59842.18108351137954497.30.21650.21650.2140.2666RANDOM51.7039
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]
0.050.020.05-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.32
r_dihedral_angle_4_deg19.739
r_dihedral_angle_3_deg17.032
r_dihedral_angle_1_deg6.216
r_scangle_it1.7
r_angle_refined_deg1.246
r_scbond_it1.088
r_mcangle_it0.908
r_mcbond_it0.497
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.32
r_dihedral_angle_4_deg19.739
r_dihedral_angle_3_deg17.032
r_dihedral_angle_1_deg6.216
r_scangle_it1.7
r_angle_refined_deg1.246
r_scbond_it1.088
r_mcangle_it0.908
r_mcbond_it0.497
r_nbtor_refined0.311
r_nbd_refined0.192
r_symmetry_hbond_refined0.177
r_symmetry_vdw_refined0.172
r_xyhbond_nbd_refined0.128
r_chiral_restr0.082
r_bond_refined_d0.008
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2544
Nucleic Acid Atoms
Solvent Atoms4
Heterogen Atoms152

Software

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