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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 1U72 PDB entry 1u72
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 287 100 mM K2PO4, 60% saturated ammoinium sulfate, 3% v/v ethanol, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Crystal Properties Matthews coefficient Solvent content 2.49 50.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.351 α = 90 b = 84.351 β = 90 c = 77.656 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 26 100 0.061 0.064 21.4 8.9 45270 42985 2 2 27.7
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) 1.35 1.42 100 0.405 0.432 4.7 8.4 6622
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 1u72 1.35 26.01 2 2 45693 42985 2282 99.99 0.18905 0.18801 0.185 0.2081 0.2058 RANDOM 16.509
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.087 r_dihedral_angle_4_deg 17.134 r_dihedral_angle_3_deg 14.73 r_dihedral_angle_1_deg 6.84 r_scangle_it 5.365 r_scbond_it 4.104 r_angle_refined_deg 2.922 r_mcangle_it 2.658 r_mcbond_it 1.625 r_chiral_restr 0.211
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.087 r_dihedral_angle_4_deg 17.134 r_dihedral_angle_3_deg 14.73 r_dihedral_angle_1_deg 6.84 r_scangle_it 5.365 r_scbond_it 4.104 r_angle_refined_deg 2.922 r_mcangle_it 2.658 r_mcbond_it 1.625 r_chiral_restr 0.211 r_bond_refined_d 0.034 r_gen_planes_refined 0.017
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1502 Nucleic Acid Atoms Solvent Atoms 237 Heterogen Atoms 98
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling