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Quadruple mutant (N51I+C59R+S108N+I164L) Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS V1/S) complexed with FB6, 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 297 0.1M Sodium malonate, pH5.0, 14% Polyethylene glycol 4000
Crystal Properties Matthews coefficient Solvent content 2.57 52.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.064 α = 90 b = 156.496 β = 90 c = 164.865 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 2021-09-10 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 2.4 24.63 99.1 0.135 0.995 9.1 5.9 59549 31.73
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.45 92.5 0.873 2 5.6
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 FREE R-VALUE 2.4 24.629 58306 2903 97.567 0.221 0.2171 0.2233 0.2909 0.2918 RANDOM 40.802
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] 0.51 -0.421 -0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.167 r_dihedral_angle_6_deg 14.102 r_dihedral_angle_2_deg 10.508 r_lrange_it 9.965 r_lrange_other 9.961 r_dihedral_angle_1_deg 7.754 r_scangle_it 5.984 r_scangle_other 5.983 r_mcangle_it 5.475 r_mcangle_other 5.475
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.167 r_dihedral_angle_6_deg 14.102 r_dihedral_angle_2_deg 10.508 r_lrange_it 9.965 r_lrange_other 9.961 r_dihedral_angle_1_deg 7.754 r_scangle_it 5.984 r_scangle_other 5.983 r_mcangle_it 5.475 r_mcangle_other 5.475 r_scbond_it 3.809 r_scbond_other 3.784 r_mcbond_it 3.567 r_mcbond_other 3.567 r_angle_refined_deg 1.819 r_dihedral_angle_other_2_deg 0.966 r_angle_other_deg 0.618 r_nbd_other 0.256 r_nbd_refined 0.221 r_symmetry_nbd_refined 0.212 r_symmetry_nbd_other 0.201 r_nbtor_refined 0.196 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.087 r_symmetry_nbtor_other 0.084 r_symmetry_xyhbond_nbd_refined 0.072 r_symmetry_xyhbond_nbd_other 0.045 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8684 Nucleic Acid Atoms Solvent Atoms 351 Heterogen Atoms 208
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction PROTEUM PLUS data scaling PHASER phasing