☰ Navigation Tabs
Alternate Binding Modes Observed for the E- and Z-Isomers of 2,4-Diaminofuro[2,3-d]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 2.25 45.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.432 α = 90 b = 61.012 β = 117.79 c = 43.217 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 2005-05-24 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 2.05 23.85 94.8 0.063 0.079 14.6 2.8 10815 1 31
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 2.05 2.1 92.8 0.32 0.32 2.6 2.8
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 2.05 21.57 1 10812 536 94.2 0.191 0.187 0.1874 0.269 0.2627 RANDOM 32.48
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] -0.02 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.375 r_dihedral_angle_3_deg 21.055 r_dihedral_angle_4_deg 18.387 r_dihedral_angle_1_deg 9.958 r_scangle_it 4.525 r_scbond_it 3.171 r_angle_refined_deg 2.632 r_mcangle_it 2.089 r_mcbond_it 1.311 r_symmetry_hbond_refined 0.403
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.375 r_dihedral_angle_3_deg 21.055 r_dihedral_angle_4_deg 18.387 r_dihedral_angle_1_deg 9.958 r_scangle_it 4.525 r_scbond_it 3.171 r_angle_refined_deg 2.632 r_mcangle_it 2.089 r_mcbond_it 1.311 r_symmetry_hbond_refined 0.403 r_nbtor_refined 0.321 r_nbd_refined 0.254 r_xyhbond_nbd_refined 0.237 r_symmetry_vdw_refined 0.225 r_chiral_restr 0.168 r_bond_refined_d 0.024 r_gen_planes_refined 0.01 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1513 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 70
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling