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Structure of the Plasmodium falciparum falcipain 2 protease in complex with an (E)-chalcone inhibitor.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OUL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 Mother liquor comprising 0.12 M of monosaccharides mixture (D-glucose; D-mannose; D-galactose; L-fucose; D-xylose; N-acetyl-D-glucosamine), 0.1 M Tris/Bicine (pH 8.5); 20% v/v glycerol, 10% w/v PEG 4000. Crystal soaked for 2 hours with (E)-chalcone #48 inhibitor. Inhibitor prepared in 100% DMSO, 100 mM concentration and then diluted to 1 mM in mother liquor for crystal soaking.
Crystal Properties Matthews coefficient Solvent content 3.43 64.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.431 α = 90 b = 109.431 β = 90 c = 107.254 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 EIGER2 X 16M 2019-01-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 3.45 94.77 90.2 0.204 0.209 0.048 1 10.7 18.9 6001 147.87
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 3.45 3.85 66.9 2.31 2.378 0.554 0.44 1.5 17.6
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2OUL 3.45 94.77 5712 288 59.2 0.258 0.255 0.2729 0.308 0.3084 Random selection
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3793 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 44
Software Software Software Name Purpose BUSTER refinement XDS data reduction autoPROC data scaling PHASER phasing