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Quadruple mutant (N51I+C59R+S108N+I164L) Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS V1/S) complexed with FB8, NADPH and dUMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DP3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 4.6 297 0.1 M Sodium acetate, pH 4.6, 0.2 M Ammonium acetate, 12% Polyethylene glycol 4000
Crystal Properties Matthews coefficient Solvent content 2.59 52.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.763 α = 90 b = 156.41 β = 90 c = 165.065 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 2022-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER TURBO X-RAY SOURCE 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.1 26.1 99.32 0.082 0.998 13.5 5.9 88097
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 100 0.487 0.915 2.4 4.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.1 26.096 87705 4422 99.352 0.197 0.1945 0.2036 0.2404 0.2452 RANDOM 33.374
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] -0.144 0.037 0.108
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.47 r_dihedral_angle_3_deg 14.045 r_dihedral_angle_2_deg 11.763 r_lrange_it 8.301 r_lrange_other 8.264 r_dihedral_angle_1_deg 7.46 r_scangle_it 5.847 r_scangle_other 5.847 r_mcangle_it 4.357 r_mcangle_other 4.357
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.47 r_dihedral_angle_3_deg 14.045 r_dihedral_angle_2_deg 11.763 r_lrange_it 8.301 r_lrange_other 8.264 r_dihedral_angle_1_deg 7.46 r_scangle_it 5.847 r_scangle_other 5.847 r_mcangle_it 4.357 r_mcangle_other 4.357 r_scbond_it 3.795 r_scbond_other 3.787 r_mcbond_it 2.988 r_mcbond_other 2.987 r_dihedral_angle_other_2_deg 2.735 r_angle_refined_deg 1.834 r_angle_other_deg 0.613 r_nbd_other 0.224 r_symmetry_nbd_refined 0.223 r_nbd_refined 0.215 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.19 r_xyhbond_nbd_refined 0.156 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.083 r_symmetry_xyhbond_nbd_refined 0.079 r_symmetry_xyhbond_nbd_other 0.075 r_gen_planes_refined 0.01 r_bond_refined_d 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8676 Nucleic Acid Atoms Solvent Atoms 588 Heterogen Atoms 198
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data collection Coot model building PHASER phasing PROTEUM PLUS data reduction PROTEUM PLUS data scaling