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Crystal structure of Plasmepsin X from Plasmodium falciparum in complex with WM382
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7TBB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 12.5% (v/v) 2-methyl-2,4-pentanediol, 0.1M bicine-tris pH 8.5, 2.85% (v/v) diethylene glycol, 6.35% (v/v) pentaethylene glycol, 12.5% (w/v) polyethylene glycol 1000, 12.5% (w/v) polyethylene glycol 3350, 5.2% (v/v) tetraethylene glycol, 4.1% (v/v) triethylene glycol
Crystal Properties Matthews coefficient Solvent content 4.75 74.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.32 α = 90 b = 109.32 β = 90 c = 118.31 γ = 120
Symmetry Space Group P 32 2 1
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 EIGER X 16M 2020-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95373 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.76 49.63 99 0.03 0.999 12.5 22.6 21289 96.22
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.76 2.91 93.6 0.496 0.936 6.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7TBB 2.76 49.62 1.34 21260 1061 98.87 0.1982 0.1966 0.1981 0.228 0.2334 91.48
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 f_dihedral_angle_d 16.6885 f_angle_d 0.5613 f_chiral_restr 0.0489 f_plane_restr 0.0041 f_bond_d 0.0025
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2659 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 124
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing