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Perferential 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 PDB entry 1u70
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 298 100 mM K2PO4 with 60% satrated ammonium sulfate with 3% v/v ethanol, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.51 51.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.5 α = 90 b = 84.5 β = 90 c = 78.131 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 CCD MARMOSAIC 325 mm CCD mirrors 2008-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.975 SSRL BL9-2
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 1.35 26.6 100 0.118 0.125 12.5 8.9 45693 45693 2 2 28
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 1.35 1.42 100 0.029 0.01 0.9 8.5 6687
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 1u70 1.35 26.71 2 2 45693 43214 2302 99.61 0.19896 0.19767 0.192 0.22341 0.2177 RANDOM 21.681
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.586 r_dihedral_angle_3_deg 14.825 r_dihedral_angle_4_deg 12.655 r_dihedral_angle_1_deg 6.948 r_scangle_it 5.317 r_scbond_it 3.618 r_angle_refined_deg 2.765 r_mcangle_it 2.552 r_mcbond_it 1.581 r_chiral_restr 0.193
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.586 r_dihedral_angle_3_deg 14.825 r_dihedral_angle_4_deg 12.655 r_dihedral_angle_1_deg 6.948 r_scangle_it 5.317 r_scbond_it 3.618 r_angle_refined_deg 2.765 r_mcangle_it 2.552 r_mcbond_it 1.581 r_chiral_restr 0.193 r_bond_refined_d 0.031 r_gen_planes_refined 0.016
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1502 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 92
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling