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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
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U70
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 298 100 mM K2PO4, 60% saturated ammonium sulfate, 3% v/v ethanol, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.49 50.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.998 α = 90 b = 83.998 β = 90 c = 78.273 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 200 IMAGE PLATE RIGAKU RAXIS IV mirrors 2008-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.54198
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.9 26.1 99.8 0.055 0.064 14.4 3.5 16181 15367 2 2 28.6
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) Redundancy Number Unique Reflections (All) 1 1.9 2 98.6 0.16 0.19 6 3.1 2311
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 17u0 1.9 26.09 2 2 15367 15363 811 99.79 0.19536 0.19278 0.1917 0.2456 0.2417 RANDOM 16.456
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 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.116 r_dihedral_angle_4_deg 17.265 r_dihedral_angle_3_deg 16.464 r_dihedral_angle_1_deg 6.712 r_scangle_it 5.347 r_scbond_it 3.554 r_angle_refined_deg 2.354 r_mcangle_it 2.205 r_mcbond_it 1.292 r_chiral_restr 0.216
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.116 r_dihedral_angle_4_deg 17.265 r_dihedral_angle_3_deg 16.464 r_dihedral_angle_1_deg 6.712 r_scangle_it 5.347 r_scbond_it 3.554 r_angle_refined_deg 2.354 r_mcangle_it 2.205 r_mcbond_it 1.292 r_chiral_restr 0.216 r_bond_refined_d 0.025 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1502 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 78
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling