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Crystal structure of a designed single-component Plasmodium falciparum AMA1-RON2L insertion fusion immunogen 3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZWZ Crystal structure of Plasmodium falciparum AMA1 in complex with a 39aa PfRON2 peptide
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291.15 0.2 M Magnesium chloride, 0.1 M Tris (pH 8.5), 20 % (w/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 1.89 36.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.36 α = 90 b = 62.92 β = 96.25 c = 60.01 γ = 90
Symmetry Space Group P 1 21 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 2021-04-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
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 2.1 19.71 98.4 0.0686 0.082 0.0445 0.994 12.07 3.2 17236 27.93
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 2.101 2.176 92.38 0.1663 0.2019 0.113 0.953 5.41 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.1 19.71 1.44 17236 862 98.4 0.1719 0.1696 0.1695 0.2157 0.2157 34.6
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 10.4404 f_angle_d 0.4816 f_chiral_restr 0.0422 f_plane_restr 0.0035 f_bond_d 0.0021
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2466 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms
Software Software Software Name Purpose SERGUI data collection XDS data reduction XDS data scaling PHENIX phasing Coot model building PHENIX refinement