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Quadruple mutant (N51I+C59R+S108N+I164L) plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with compound 42 and NADPH
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 4.6 298 0.1M sodium acetate, pH 4.6, 0.2M ammonium acetate, 25% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.61 52.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.308 α = 90 b = 154.488 β = 90 c = 163.939 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 CCD Nonius Kappa CCD 2003-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ENRAF-NONIUS FR591 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 2.59 10 90.8 0.071 14.5 3.99 40994
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 2.74 0.479
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 4DP3 2.59 10 40185 2053 88.369 0.193 0.1889 0.1941 0.2609 0.2588 39.937
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] 1.514 -1.818 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.278 r_dihedral_angle_4_deg 18.488 r_dihedral_angle_3_deg 18.19 r_dihedral_angle_1_deg 9.078 r_lrange_other 8.958 r_lrange_it 8.957 r_mcangle_it 6.404 r_mcangle_other 6.404 r_scangle_it 5.598 r_scangle_other 5.598
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.278 r_dihedral_angle_4_deg 18.488 r_dihedral_angle_3_deg 18.19 r_dihedral_angle_1_deg 9.078 r_lrange_other 8.958 r_lrange_it 8.957 r_mcangle_it 6.404 r_mcangle_other 6.404 r_scangle_it 5.598 r_scangle_other 5.598 r_mcbond_it 3.972 r_mcbond_other 3.965 r_scbond_it 3.544 r_scbond_other 3.544 r_angle_refined_deg 1.79 r_angle_other_deg 1.259 r_chiral_restr_other 0.753 r_nbd_other 0.24 r_symmetry_nbd_refined 0.222 r_nbd_refined 0.215 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.162 r_symmetry_xyhbond_nbd_refined 0.153 r_chiral_restr 0.116 r_symmetry_nbtor_other 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_symmetry_xyhbond_nbd_other 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8875 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 194
Software Software Software Name Purpose REFMAC refinement DENZO data reduction Coot model building HKL-2000 data scaling