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Crystal structure of Trypanosoma cruzi Dihydrofolate Reductase-Thymidylate Synthase in complex with (6S)-5,6,7,8-TETRAHYDROFOLATE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3INV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 298 TcDHFR-TS 12.5 mg ml-1 in 25 mMTris pH 7.2 and 80 mMNaCl, precipitant solution 12% (w/v) PEG 3350, 100 mM sodium malonate pH 5
Crystal Properties Matthews coefficient Solvent content 2.63 53.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.547 α = 90 b = 173.54 β = 90 c = 174.159 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2015-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96861 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 86.77 99.5 9.2 6.5 213627 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3INV 1.8 86.77 202617 10547 99.23 0.17906 0.1769 0.21991 0.2535 RANDOM 26.495
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 33.032 r_dihedral_angle_4_deg 18.545 r_dihedral_angle_3_deg 14.54 r_long_range_B_refined 7.974 r_dihedral_angle_1_deg 6.481 r_scbond_it 3.828 r_mcangle_it 3.644 r_mcbond_it 2.748 r_angle_refined_deg 2.392 r_chiral_restr 0.202
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.032 r_dihedral_angle_4_deg 18.545 r_dihedral_angle_3_deg 14.54 r_long_range_B_refined 7.974 r_dihedral_angle_1_deg 6.481 r_scbond_it 3.828 r_mcangle_it 3.644 r_mcbond_it 2.748 r_angle_refined_deg 2.392 r_chiral_restr 0.202 r_bond_refined_d 0.026 r_gen_planes_refined 0.014 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15441 Nucleic Acid Atoms Solvent Atoms 2024 Heterogen Atoms 588
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing