3NXV

Preferential Selection of Isomer Binding from Chiral Mixtures: Alternate Binding Modes Observed for the E- and Z-isomers of a Series of 5-Substituted 2,4-Diaminofuro[2,3-d]pyrimidines as Ternary Complexes with NADPH and Human Dihydrofolate Reductase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1U70 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.9298100 mM K2PO4, 60% saturated ammonium sulfate, 3% v/v ethanol, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4950.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.998α = 90
b = 83.998β = 90
c = 78.273γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200IMAGE PLATERIGAKU RAXIS IVmirrors2008-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.54198

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
11.926.199.80.0550.06414.43.516181153672228.6
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)
11.9298.60.160.1963.12311

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)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 REPLACEMENTTHROUGHOUTPDB entry 17u01.926.0922153671536381199.790.195360.192780.2456RANDOM16.456
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]
-0.01-0.01-0.010.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.116
r_dihedral_angle_4_deg17.265
r_dihedral_angle_3_deg16.464
r_dihedral_angle_1_deg6.712
r_scangle_it5.347
r_scbond_it3.554
r_angle_refined_deg2.354
r_mcangle_it2.205
r_mcbond_it1.292
r_chiral_restr0.216
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.116
r_dihedral_angle_4_deg17.265
r_dihedral_angle_3_deg16.464
r_dihedral_angle_1_deg6.712
r_scangle_it5.347
r_scbond_it3.554
r_angle_refined_deg2.354
r_mcangle_it2.205
r_mcbond_it1.292
r_chiral_restr0.216
r_bond_refined_d0.025
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1502
Nucleic Acid Atoms
Solvent Atoms92
Heterogen Atoms78

Software

Software
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling