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Structure of full-length amyloidogenic immunoglobulin light chain H9 in complex with 4-(3-ethyl-3-phenylpyrrolidin-1-yl)-1,6-dimethylpyridin-2(1H)-one
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8FO4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 20% PEG3350, 0.2 M potassium phosphate monobasic, 4 degrees C
Crystal Properties Matthews coefficient Solvent content 2.75 55.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.967 α = 84.408 b = 63.708 β = 86.906 c = 86.261 γ = 80.632
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 2021-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 APS 23-ID-B
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 2.2 48.53 91.4 0.068 0.079 0.041 0.998 10.2 3.7 44680 40.85
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 2.2 2.27 80.2 0.736 0.864 0.449 0.793 2 3.6
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 2.2 48.53 1.96 44609 2210 91.3 0.2344 0.2319 0.2329 0.2842 0.2845 59.51
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 13.6291 f_angle_d 0.5586 f_chiral_restr 0.0434 f_plane_restr 0.0037 f_bond_d 0.0035
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6324 Nucleic Acid Atoms Solvent Atoms 253 Heterogen Atoms 79
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHASER phasing