3K45

Alternate Binding Modes Observed for the E- and Z-isomers of 2,4-Diaminofuro[2,3d]pyrimidines as Ternary Complexes with NADPH and Mouse Dihydrofolate Reductase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FZJPDB ENTRY 2FZJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.3200 MM TRIS, PH 8.3, 85 MM NA CACODYLATE, 25% PEG 4K, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Crystal Properties
Matthews coefficientSolvent content
2.2745.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.358α = 90
b = 61.094β = 117.13
c = 43.304γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200IMAGE PLATERIGAKU RAXIS IV2007-08-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200

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
11.617.8298.50.0740.78.22.424297133.2
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)
11.61.6495.30.390.493.31.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2FZJ1.617.82123070122795.80.1980.1960.242RANDOM33.86
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
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.825
r_dihedral_angle_4_deg18.799
r_dihedral_angle_3_deg17.876
r_dihedral_angle_1_deg5.844
r_sphericity_free5.6
r_scangle_it3.584
r_sphericity_bonded3.368
r_scbond_it2.719
r_rigid_bond_restr2.004
r_mcangle_it1.948
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.825
r_dihedral_angle_4_deg18.799
r_dihedral_angle_3_deg17.876
r_dihedral_angle_1_deg5.844
r_sphericity_free5.6
r_scangle_it3.584
r_sphericity_bonded3.368
r_scbond_it2.719
r_rigid_bond_restr2.004
r_mcangle_it1.948
r_angle_refined_deg1.843
r_mcbond_it1.307
r_nbtor_refined0.316
r_symmetry_vdw_refined0.26
r_nbd_refined0.204
r_xyhbond_nbd_refined0.159
r_symmetry_hbond_refined0.134
r_chiral_restr0.12
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1489
Nucleic Acid Atoms
Solvent Atoms181
Heterogen Atoms69

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
d*TREKdata reduction
SCALAdata scaling