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Wild-type plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with fragment 148, NADPH, and dUMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DPD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 4.6 297 0.1M NaOAc, 0.17 M Ammonium acetate, 18% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.53 56.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.638 α = 90 b = 155.639 β = 90 c = 164.614 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CMOS BRUKER PHOTON 100 2019-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.65 24.83 97.9 0.1612 10.3 5.85 42316
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.7 99.9 0.5087 4.65
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE 4DPD 2.65 24.826 42316 2095 97.82 0.258 0.255 0.198 0.3245 0.2695 31.691
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] -0.229 -3.457 3.686
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.6 r_dihedral_angle_4_deg 20.533 r_dihedral_angle_3_deg 19.155 r_dihedral_angle_1_deg 9.037 r_lrange_it 7.347 r_lrange_other 7.347 r_mcangle_it 5.062 r_mcangle_other 5.062 r_scangle_it 4.728 r_scangle_other 4.728
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.6 r_dihedral_angle_4_deg 20.533 r_dihedral_angle_3_deg 19.155 r_dihedral_angle_1_deg 9.037 r_lrange_it 7.347 r_lrange_other 7.347 r_mcangle_it 5.062 r_mcangle_other 5.062 r_scangle_it 4.728 r_scangle_other 4.728 r_mcbond_it 3.107 r_mcbond_other 3.107 r_scbond_it 2.881 r_scbond_other 2.881 r_angle_other_deg 2.342 r_angle_refined_deg 1.843 r_symmetry_nbd_refined 0.277 r_nbd_other 0.27 r_symmetry_nbd_other 0.223 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.19 r_nbtor_refined 0.18 r_symmetry_xyhbond_nbd_other 0.141 r_symmetry_xyhbond_nbd_refined 0.138 r_chiral_restr 0.077 r_symmetry_nbtor_other 0.076 r_bond_other_d 0.035 r_bond_refined_d 0.011 r_gen_planes_other 0.011 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8867 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 158
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction Coot model building