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Crystal structure of Plasmodium falciparum Plasmepsin X in complex with the hydroxyethylamine drug 7k.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7TBC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 293.15 20% [w/v] PEG 4000, 0.2 M Magnesium sulfate, 10% [w/v] Glycerol
Crystal Properties Matthews coefficient Solvent content 3.34 63.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.95 α = 90 b = 147.95 β = 90 c = 147.95 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2023-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 1.00 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.7 104.62 100 0.1 0.102 0.022 1 22.6 40.4 59002
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 1.7 1.73 6.873 7.047 1.557 0.303 40.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FREE R-VALUE 1.7 104.616 58992 2835 99.997 0.197 0.1952 0.1952 0.2265 0.2269 42.21
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.92 r_dihedral_angle_6_deg 14.786 r_dihedral_angle_3_deg 12.084 r_lrange_it 8.29 r_lrange_other 8.258 r_dihedral_angle_1_deg 7.795 r_dihedral_angle_other_2_deg 6.36 r_scangle_it 5.895 r_scangle_other 5.866 r_mcangle_other 4.335
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.92 r_dihedral_angle_6_deg 14.786 r_dihedral_angle_3_deg 12.084 r_lrange_it 8.29 r_lrange_other 8.258 r_dihedral_angle_1_deg 7.795 r_dihedral_angle_other_2_deg 6.36 r_scangle_it 5.895 r_scangle_other 5.866 r_mcangle_other 4.335 r_mcangle_it 4.333 r_scbond_it 4.146 r_scbond_other 4.121 r_mcbond_it 3.152 r_mcbond_other 3.15 r_angle_refined_deg 2.067 r_angle_other_deg 0.824 r_symmetry_nbd_refined 0.438 r_xyhbond_nbd_refined 0.248 r_nbd_refined 0.187 r_nbtor_refined 0.174 r_symmetry_nbd_other 0.17 r_nbd_other 0.149 r_chiral_restr 0.104 r_symmetry_xyhbond_nbd_refined 0.083 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2538 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction Aimless data scaling PHASER phasing