3EEJ

Candida glabrata Dihydrofolate Reductase complexed with 2,4-diamino-5-[3-methyl-3-(3-methoxy-5-phenylphenyl)prop-1-ynyl]-6-methylpyrimidine(UCP111D) and NADPH


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5277PEG4000, MgCl2, pH 8.5, vapor diffusion, hanging drop, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.0138.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.871α = 90
b = 42.871β = 90
c = 231.485γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCD2008-02-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X25NSLSX25

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.15098.80.05536.0434.423986
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.1892.20.1084.32248

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUT2.1137.4823906122199.50.170.1670.229RANDOM16.907
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_deg37.066
r_dihedral_angle_1_deg31.619
r_dihedral_angle_3_deg18.257
r_dihedral_angle_4_deg17.13
r_scangle_it4.615
r_scbond_it3.276
r_angle_refined_deg2.268
r_mcangle_it1.907
r_mcbond_it1.367
r_symmetry_vdw_refined0.328
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.066
r_dihedral_angle_1_deg31.619
r_dihedral_angle_3_deg18.257
r_dihedral_angle_4_deg17.13
r_scangle_it4.615
r_scbond_it3.276
r_angle_refined_deg2.268
r_mcangle_it1.907
r_mcbond_it1.367
r_symmetry_vdw_refined0.328
r_nbtor_refined0.311
r_nbd_refined0.216
r_symmetry_hbond_refined0.205
r_chiral_restr0.185
r_xyhbond_nbd_refined0.178
r_bond_refined_d0.022
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3692
Nucleic Acid Atoms
Solvent Atoms190
Heterogen Atoms150

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection