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Wild type plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS), fragment 263, NADP+, dUMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DPD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 5 297 0.1M Na malonate, 13%PEG4000
Crystal Properties Matthews coefficient Solvent content 2.5864038 52.473164
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.143 α = 90 b = 154.088 β = 90 c = 163.598 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 2019-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 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 2.641 24.527 96.7 0.0927 12.68 4.66 34592 17.16
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 2.8 2.94 88.4 0.1876
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 4DPD 2.8 20.7 34591 1686 81.167 0.238 0.2343 0.2044 0.3031 0.2784 27.023
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] -3.219 11.71 -8.491
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.128 r_dihedral_angle_3_deg 19.933 r_dihedral_angle_4_deg 17.233 r_dihedral_angle_1_deg 9.063 r_lrange_it 6.266 r_lrange_other 6.266 r_mcangle_other 4.166 r_mcangle_it 4.165 r_scangle_other 3.459 r_scangle_it 3.416
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.128 r_dihedral_angle_3_deg 19.933 r_dihedral_angle_4_deg 17.233 r_dihedral_angle_1_deg 9.063 r_lrange_it 6.266 r_lrange_other 6.266 r_mcangle_other 4.166 r_mcangle_it 4.165 r_scangle_other 3.459 r_scangle_it 3.416 r_mcbond_it 2.465 r_mcbond_other 2.464 r_angle_other_deg 2.365 r_scbond_it 1.976 r_scbond_other 1.976 r_angle_refined_deg 1.647 r_chiral_restr_other 1.46 r_nbd_other 0.306 r_symmetry_nbd_refined 0.283 r_symmetry_nbd_other 0.226 r_nbd_refined 0.221 r_xyhbond_nbd_refined 0.201 r_nbtor_refined 0.179 r_symmetry_xyhbond_nbd_refined 0.114 r_symmetry_xyhbond_nbd_other 0.107 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.07 r_bond_other_d 0.035 r_bond_refined_d 0.008 r_gen_planes_other 0.008 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8658 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data scaling Coot model building PROTEUM PLUS data reduction