3SH2

Staphylococcus aureus Dihydrofolate Reductase complexed with NADPH and 6-ethyl-5-(3-(4-methoxybiphenyl-3-yl)prop-1-ynyl)pyrimidine-2,4-diamine (UCP120J)


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
2.8656.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.163α = 90
b = 86.163β = 90
c = 103.24γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77.2CCDADSC QUANTUM 3152010-05-03M
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
12.99937.3299.910.1730.17320.25.6834979313357.84
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)
12.9993.11000.490.493.25.4418

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)2.99937.328349793141899.910.21810.21810.21650.2496RANDOM57.8438
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]
-0.04-0.02-0.040.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.592
r_dihedral_angle_3_deg16.669
r_dihedral_angle_4_deg14.414
r_dihedral_angle_1_deg4.88
r_angle_refined_deg0.983
r_scangle_it0.463
r_mcangle_it0.405
r_nbtor_refined0.301
r_scbond_it0.252
r_mcbond_it0.223
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.592
r_dihedral_angle_3_deg16.669
r_dihedral_angle_4_deg14.414
r_dihedral_angle_1_deg4.88
r_angle_refined_deg0.983
r_scangle_it0.463
r_mcangle_it0.405
r_nbtor_refined0.301
r_scbond_it0.252
r_mcbond_it0.223
r_nbd_refined0.155
r_symmetry_vdw_refined0.142
r_xyhbond_nbd_refined0.104
r_chiral_restr0.065
r_bond_refined_d0.006
r_symmetry_hbond_refined0.006
r_gen_planes_refined0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2544
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms150

Software

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