4H95

Candida albicans dihydrofolate reductase complexed with NADPH and 6-ethyl-5-{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 modelPDB 1AOE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5277PEG 3350, KMES, glycine, pH 6.5, vapor diffusion, hanging drop, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.1761.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.482α = 90
b = 118.856β = 90
c = 39.284γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2010-11-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
12.653.0299.70.1158.36.1177691776933
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)
12.62.6999.90.50736.311725

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1AOE2.641.96176701767092598.250.24070.24040.2676RANDOM53.5495
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]
1.51-4.523.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.676
r_dihedral_angle_3_deg14.146
r_dihedral_angle_4_deg14.009
r_dihedral_angle_1_deg4.999
r_angle_refined_deg0.97
r_scangle_it0.865
r_mcangle_it0.492
r_scbond_it0.468
r_mcbond_it0.268
r_chiral_restr0.061
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.676
r_dihedral_angle_3_deg14.146
r_dihedral_angle_4_deg14.009
r_dihedral_angle_1_deg4.999
r_angle_refined_deg0.97
r_scangle_it0.865
r_mcangle_it0.492
r_scbond_it0.468
r_mcbond_it0.268
r_chiral_restr0.061
r_bond_refined_d0.006
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3078
Nucleic Acid Atoms
Solvent Atoms12
Heterogen Atoms152

Software

Software
Software NamePurpose
d*TREKdata scaling
d*TREKdata reduction
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection