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Quadruple mutant (N51I+C59R+S108N+I164L) plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with B12155 inhibitor
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 298 NaOAc, NH2OAc, PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.61 52.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.902 α = 90 b = 156.504 β = 90 c = 165.484 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 123 CCD ADSC QUANTUM 315 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 2.1 50 99.1 0.056 0.061 0.024 14.4 6.2 88221
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.18 96.5 0.449 0.49 0.193 0.931 6
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 2.1 26.988 86619 4377 97.16 0.197 0.195 0.2411 0.2415 34.067
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] -0.021 0.129 -0.108
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.485 r_dihedral_angle_4_deg 17.127 r_dihedral_angle_3_deg 16.434 r_dihedral_angle_1_deg 8.297 r_lrange_other 7.9 r_lrange_it 7.894 r_scangle_it 5.432 r_scangle_other 5.432 r_mcangle_it 4.946 r_mcangle_other 4.945
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.485 r_dihedral_angle_4_deg 17.127 r_dihedral_angle_3_deg 16.434 r_dihedral_angle_1_deg 8.297 r_lrange_other 7.9 r_lrange_it 7.894 r_scangle_it 5.432 r_scangle_other 5.432 r_mcangle_it 4.946 r_mcangle_other 4.945 r_scbond_it 3.528 r_scbond_other 3.528 r_mcbond_it 3.27 r_mcbond_other 3.27 r_chiral_restr_other 2.062 r_angle_refined_deg 1.715 r_angle_other_deg 1.384 r_nbd_other 0.261 r_nbd_refined 0.21 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.177 r_symmetry_nbd_refined 0.177 r_xyhbond_nbd_refined 0.156 r_symmetry_xyhbond_nbd_refined 0.156 r_chiral_restr 0.086 r_symmetry_xyhbond_nbd_other 0.082 r_symmetry_nbtor_other 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8894 Nucleic Acid Atoms Solvent Atoms 332 Heterogen Atoms 212
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing