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Quadruple mutant (N51I+C59R+S108N+I164L) plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with B12128 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 4.5 297 NaOAc, NH2OAc, PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.71 54.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.176 α = 90 b = 156.175 β = 90 c = 165.08 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 ADSC QUANTUM 315r 2016-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.149 50 85 0.058 0.067 0.033 19.75 3.7 67136
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 2.15 2.23 86.2 0.403 0.908 3.1
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE 4DP3 2.149 45.047 66982 3355 82.177 0.196 0.1936 0.249 0.2441 31.803
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] 0.516 -0.081 -0.435
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.702 r_dihedral_angle_3_deg 16.657 r_dihedral_angle_4_deg 15.685 r_dihedral_angle_1_deg 8.303 r_lrange_it 7.185 r_lrange_other 7.18 r_scangle_it 4.68 r_scangle_other 4.68 r_mcangle_it 4.328 r_mcangle_other 4.328
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.702 r_dihedral_angle_3_deg 16.657 r_dihedral_angle_4_deg 15.685 r_dihedral_angle_1_deg 8.303 r_lrange_it 7.185 r_lrange_other 7.18 r_scangle_it 4.68 r_scangle_other 4.68 r_mcangle_it 4.328 r_mcangle_other 4.328 r_scbond_it 3 r_scbond_other 2.994 r_mcbond_it 2.786 r_mcbond_other 2.786 r_chiral_restr_other 1.973 r_angle_refined_deg 1.702 r_angle_other_deg 1.314 r_symmetry_nbd_refined 0.251 r_nbd_other 0.218 r_nbd_refined 0.211 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.176 r_symmetry_xyhbond_nbd_refined 0.161 r_chiral_restr 0.126 r_symmetry_xyhbond_nbd_other 0.094 r_symmetry_nbtor_other 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8722 Nucleic Acid Atoms Solvent Atoms 316 Heterogen Atoms 196
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing