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Alternate Binding Modes Observed for the E- and Z-isomers of 2,4-Diaminofuro[2,3d]pyrimidines as Ternary Complexes with NADPH and Mouse Dihydrofolate Reductase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FZJ PDB ENTRY 2FZJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.3 200 MM TRIS, PH 8.3, 85 MM NA CACODYLATE, 25% PEG 4K, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Crystal Properties Matthews coefficient Solvent content 2.27 45.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.358 α = 90 b = 61.094 β = 117.13 c = 43.304 γ = 90
Symmetry Space Group P 1 21 1
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 2007-08-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 1.6 17.82 98.5 0.074 0.7 8.2 2.4 24297 1 33.2
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 1.6 1.64 95.3 0.39 0.49 3.3 1.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 2FZJ 1.6 17.82 1 23070 1227 95.8 0.198 0.196 0.2104 0.242 0.2547 RANDOM 33.86
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 35.825 r_dihedral_angle_4_deg 18.799 r_dihedral_angle_3_deg 17.876 r_dihedral_angle_1_deg 5.844 r_sphericity_free 5.6 r_scangle_it 3.584 r_sphericity_bonded 3.368 r_scbond_it 2.719 r_rigid_bond_restr 2.004 r_mcangle_it 1.948
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.825 r_dihedral_angle_4_deg 18.799 r_dihedral_angle_3_deg 17.876 r_dihedral_angle_1_deg 5.844 r_sphericity_free 5.6 r_scangle_it 3.584 r_sphericity_bonded 3.368 r_scbond_it 2.719 r_rigid_bond_restr 2.004 r_mcangle_it 1.948 r_angle_refined_deg 1.843 r_mcbond_it 1.307 r_nbtor_refined 0.316 r_symmetry_vdw_refined 0.26 r_nbd_refined 0.204 r_xyhbond_nbd_refined 0.159 r_symmetry_hbond_refined 0.134 r_chiral_restr 0.12 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1489 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 69
Software Software Software Name Purpose MOLREP phasing REFMAC refinement d*TREK data reduction SCALA data scaling