3I8A

Staphylococcus aureus H30N, F98Y Dihydrofolate Reductase complexed with NADPH and 2,4-diamino-5-(3-(2,5-dimethoxyphenyl)prop-1-ynyl)-6-ethylpyrimidine (UCP120B)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.527715% PEG 10,000, 150 mM sodium acetate, 100 mM MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.7455.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.164α = 90
b = 79.164β = 90
c = 108.96γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77.2CCDADSC QUANTUM 3152009-01-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.0809NSLSX29A

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
12.4137.2295.010.040.041.110.4750475043315.689
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)
12.412.4721000.0740.0740.810.1560

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 Fourier MethodsTHROUGHOUT3FQO2.4137.227504750436395.010.2080.2080.2060.261RANDOM15.662
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]
-0.01-0.01-0.010.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.063
r_dihedral_angle_4_deg20.893
r_dihedral_angle_3_deg18.586
r_dihedral_angle_1_deg7.585
r_scangle_it2.709
r_scbond_it1.777
r_angle_refined_deg1.64
r_mcangle_it1.314
r_mcbond_it0.753
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.063
r_dihedral_angle_4_deg20.893
r_dihedral_angle_3_deg18.586
r_dihedral_angle_1_deg7.585
r_scangle_it2.709
r_scbond_it1.777
r_angle_refined_deg1.64
r_mcangle_it1.314
r_mcbond_it0.753
r_nbtor_refined0.308
r_symmetry_vdw_refined0.215
r_nbd_refined0.211
r_xyhbond_nbd_refined0.186
r_symmetry_hbond_refined0.162
r_chiral_restr0.105
r_bond_refined_d0.014
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1272
Nucleic Acid Atoms
Solvent Atoms43
Heterogen Atoms71

Software

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