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Crystal structure of the Plasmodium falciparum Apical membrane antigen (AMA1) in complex with single domain i-body WD34
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z40 experimental model PDB 5AEA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 0.1MSodium HEPES pH7.5
70% v/v MPD
Crystal Properties Matthews coefficient Solvent content 2.83 56.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.651 α = 90 b = 38.462 β = 90.18 c = 227.355 γ = 90
Symmetry Space Group I 1 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 2022-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95372 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.6 38.45 100 0.994 6.8 4.8 19822 34.06
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.693 0.864
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 2.6 38.45 1.34 19608 1010 99.92 0.2143 0.2132 0.2136 0.2348 0.2349 49.95
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 12.8642 f_angle_d 0.6029 f_chiral_restr 0.0448 f_plane_restr 0.005 f_bond_d 0.0028
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2905 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 24
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling PHASER phasing