3K47

Alternate Binding Modes Observed for the E- and Z-Isomers of 2,4-Diaminofuro[2,3-d]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
2.2545.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.432α = 90
b = 61.012β = 117.79
c = 43.217γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200IMAGE PLATERIGAKU RAXIS IV2005-05-24MSINGLE 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
12.0523.8594.80.0630.07914.62.810815131
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)
12.052.192.80.320.322.62.8

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 2FZJ2.0521.5711081253694.20.1910.1870.269RANDOM32.48
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]
-0.02-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.375
r_dihedral_angle_3_deg21.055
r_dihedral_angle_4_deg18.387
r_dihedral_angle_1_deg9.958
r_scangle_it4.525
r_scbond_it3.171
r_angle_refined_deg2.632
r_mcangle_it2.089
r_mcbond_it1.311
r_symmetry_hbond_refined0.403
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.375
r_dihedral_angle_3_deg21.055
r_dihedral_angle_4_deg18.387
r_dihedral_angle_1_deg9.958
r_scangle_it4.525
r_scbond_it3.171
r_angle_refined_deg2.632
r_mcangle_it2.089
r_mcbond_it1.311
r_symmetry_hbond_refined0.403
r_nbtor_refined0.321
r_nbd_refined0.254
r_xyhbond_nbd_refined0.237
r_symmetry_vdw_refined0.225
r_chiral_restr0.168
r_bond_refined_d0.024
r_gen_planes_refined0.01
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1513
Nucleic Acid Atoms
Solvent Atoms117
Heterogen Atoms70

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling