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Quadruple mutant plasmodium falciparum dihydrofolate reductase complexed with B10042
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 2.73 54.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.995 α = 90 b = 155.944 β = 90 c = 165.34 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 2016-10-15 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 99.7 0.032 0.038 0.02 19.8 3.8 104189
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 99.9 0.161 0.188 0.096 0.979 3.8
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 1.973 32.199 103923 5079 99.352 0.175 0.173 0.183 0.2129 0.2222 29.648
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] -0.071 0.123 -0.051
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.925 r_dihedral_angle_4_deg 17.988 r_dihedral_angle_3_deg 16.025 r_lrange_it 7.817 r_lrange_other 7.817 r_dihedral_angle_1_deg 7.671 r_scangle_it 5.63 r_scangle_other 5.616 r_mcangle_it 4.502 r_mcangle_other 4.502
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.925 r_dihedral_angle_4_deg 17.988 r_dihedral_angle_3_deg 16.025 r_lrange_it 7.817 r_lrange_other 7.817 r_dihedral_angle_1_deg 7.671 r_scangle_it 5.63 r_scangle_other 5.616 r_mcangle_it 4.502 r_mcangle_other 4.502 r_scbond_it 3.703 r_scbond_other 3.691 r_mcbond_it 3.095 r_mcbond_other 3.079 r_angle_refined_deg 1.807 r_angle_other_deg 1.401 r_chiral_restr_other 0.934 r_nbd_other 0.255 r_symmetry_nbd_refined 0.218 r_nbd_refined 0.212 r_symmetry_xyhbond_nbd_refined 0.212 r_symmetry_nbd_other 0.181 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.168 r_chiral_restr 0.144 r_symmetry_xyhbond_nbd_other 0.081 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8757 Nucleic Acid Atoms Solvent Atoms 716 Heterogen Atoms 168
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction