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Structure of full-length amyloidogenic immunoglobulin light chain H9 in complex with 2-(6-methyl-2-oxo-4-(2-phenylpropoxy)pyridin-1(2H)-yl)ethyl (3-(1H-imidazol-4-yl)benzyl)carbamate
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 2.76 55.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.422 α = 85.112 b = 63.05 β = 86.369 c = 86.525 γ = 80.681
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 PILATUS3 6M 2021-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-ID-D
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 48.61 89.7 0.098 0.139 0.098 0.976 6.3 1.8 58369 18.98
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 2.05 0.234 0.331 0.234 0.851 2.6 1.7
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 48.61 1.96 58267 2910 89.54 0.2113 0.2089 0.2092 0.2575 0.2573 25
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 13.0591 f_angle_d 0.6256 f_chiral_restr 0.0441 f_plane_restr 0.0038 f_bond_d 0.0032
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6318 Nucleic Acid Atoms Solvent Atoms 771 Heterogen Atoms 92
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHASER phasing