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Crystal structure of broadly neutralizing human monoclonal antibody 75B10 in complex with AMA1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3B2U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291.15 0.2 M calcium acetate, 0.1 M Imidazole, 20% PEG 1000
Crystal Properties Matthews coefficient Solvent content 3.19 61.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.236 α = 90 b = 93.236 β = 90 c = 228.015 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 2022-06-11 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 2.9 19.88 92.3 0.2585 0.2725 0.08541 0.987 4.5 10.1 26126 52.8
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 2.9 2.98 77.49 1.594 1.679 0.5225 0.573 0.59 10
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 2.9 19.88 0.02 24131 1843 92.29 0.2013 0.1987 0.1986 0.2319 0.2319 57
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 5.1523 f_angle_d 0.5874 f_chiral_restr 0.0448 f_plane_restr 0.0045 f_bond_d 0.0038
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5578 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms
Software Software Software Name Purpose SERGUI data collection XDS data reduction XSCALE data scaling PHENIX phasing Coot model building PHENIX refinement