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Wild-type Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with fragment 820, NADPH, 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 5 297 0.1M Na malonate, 12% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.66 53.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.185 α = 90 b = 154.73 β = 90 c = 163.816 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 2019-10-10 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 2.51 24.812 97.8 0.1395 11.7 5.68 41512
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 2.75 91.7 0.3911
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 2.51 24.812 41511 2043 83.26 0.224 0.2205 0.2041 0.2947 0.2781 28.124
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] -1.455 11.879 -10.424
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.771 r_dihedral_angle_3_deg 21.702 r_dihedral_angle_4_deg 20.549 r_dihedral_angle_1_deg 8.624 r_lrange_it 6.617 r_lrange_other 6.617 r_mcangle_it 4.221 r_mcangle_other 4.22 r_scangle_it 3.424 r_scangle_other 3.424
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.771 r_dihedral_angle_3_deg 21.702 r_dihedral_angle_4_deg 20.549 r_dihedral_angle_1_deg 8.624 r_lrange_it 6.617 r_lrange_other 6.617 r_mcangle_it 4.221 r_mcangle_other 4.22 r_scangle_it 3.424 r_scangle_other 3.424 r_mcbond_it 2.501 r_mcbond_other 2.501 r_angle_other_deg 2.334 r_scbond_it 2.011 r_scbond_other 2.007 r_angle_refined_deg 1.693 r_chiral_restr_other 1.445 r_nbd_other 0.273 r_symmetry_xyhbond_nbd_refined 0.24 r_symmetry_nbd_other 0.232 r_nbd_refined 0.214 r_symmetry_nbd_refined 0.214 r_xyhbond_nbd_refined 0.183 r_nbtor_refined 0.179 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.068 r_symmetry_xyhbond_nbd_other 0.068 r_bond_other_d 0.035 r_bond_refined_d 0.009 r_gen_planes_other 0.009 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8797 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 115
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction PROTEUM PLUS data scaling Coot model building