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Quadruple mutant (N51I+C59R+S108N+I164L) plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with B12154
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 NaOAc, NH2OAc, PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.6 52.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.885 α = 90 b = 156.288 β = 90 c = 165.288 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 1.97 50 98.8 0.055 0.06 0.024 14.3 5.9 105672
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 1.97 2.04 91 0.435 0.48 0.201 0.916 5.3
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 1.97 26.11 102018 5111 95.445 0.196 0.1943 0.2326 0.2415 33.555
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] 0.019 0.065 -0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.58 r_dihedral_angle_4_deg 16.439 r_dihedral_angle_3_deg 16.004 r_dihedral_angle_1_deg 8.24 r_lrange_other 7.886 r_lrange_it 7.884 r_scangle_it 5.69 r_scangle_other 5.689 r_mcangle_it 4.927 r_mcangle_other 4.926
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.58 r_dihedral_angle_4_deg 16.439 r_dihedral_angle_3_deg 16.004 r_dihedral_angle_1_deg 8.24 r_lrange_other 7.886 r_lrange_it 7.884 r_scangle_it 5.69 r_scangle_other 5.689 r_mcangle_it 4.927 r_mcangle_other 4.926 r_scbond_it 3.692 r_scbond_other 3.692 r_mcbond_it 3.355 r_mcbond_other 3.355 r_chiral_restr_other 1.948 r_angle_refined_deg 1.772 r_angle_other_deg 1.389 r_symmetry_nbd_refined 0.245 r_nbd_other 0.219 r_nbd_refined 0.21 r_symmetry_nbd_other 0.181 r_nbtor_refined 0.178 r_symmetry_xyhbond_nbd_refined 0.175 r_xyhbond_nbd_refined 0.159 r_chiral_restr 0.134 r_symmetry_nbtor_other 0.08 r_symmetry_xyhbond_nbd_other 0.064 r_bond_refined_d 0.012 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 8767 Nucleic Acid Atoms Solvent Atoms 422 Heterogen Atoms 202
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data scaling DENZO data reduction PHASER phasing