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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.pdb
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 298 K2PO4 with 30% saturated ammonium sulfate with 3% v/v ethanol, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.49 50.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.15 α = 90 b = 84.15 β = 90 c = 77.968 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 99.9 0.068 0.025 18.9 8.7 45729 45197 2 2 20.1
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 99.9 0.5 0.17 4.4 8.2 6605
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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.pdb 1.35 26.62 2 45197 42917 2276 99.94 0.1967 0.19223 0.19132 0.1927 0.20892 0.2058 RANDOM 16.678
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 37.888 r_dihedral_angle_4_deg 18.495 r_dihedral_angle_3_deg 14.454 r_dihedral_angle_1_deg 7.071 r_scangle_it 5.297 r_scbond_it 3.618 r_angle_refined_deg 2.788 r_mcangle_it 2.491 r_mcbond_it 1.492 r_chiral_restr 0.176
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.888 r_dihedral_angle_4_deg 18.495 r_dihedral_angle_3_deg 14.454 r_dihedral_angle_1_deg 7.071 r_scangle_it 5.297 r_scbond_it 3.618 r_angle_refined_deg 2.788 r_mcangle_it 2.491 r_mcbond_it 1.492 r_chiral_restr 0.176 r_bond_refined_d 0.034 r_gen_planes_refined 0.015
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1504 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 97
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling