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Structure of full-length amyloidogenic immunoglobulin light chain H9 in complex with 1-(1-(imidazo[1,5-a]pyrazin-8-yl)azetidin-3-yl)-3-(2-(6-methyl-4-(3-methyl-3-phenylpyrrolidin-1-yl)-2-oxopyridin-1(2H)-yl)ethyl)urea
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
Crystal Properties Matthews coefficient Solvent content 2.77 55.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.415 α = 84.354 b = 63.235 β = 85.996 c = 86.721 γ = 80.649
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 2023-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.97934 NSLS-II 17-ID-2
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 1.81 48.42 94.6 0.079 0.103 0.065 0.992 10 2.1 85151 -3 20.99
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 1.81 1.83 79.5 0.465 0.609 0.39 0.166 1.44 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 1.81 48.42 1.97 83268 4000 93.88 0.1953 0.1937 0.1948 0.2241 0.2249 28.14
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 14.4202 f_angle_d 1.7924 f_chiral_restr 0.1019 f_bond_d 0.0222 f_plane_restr 0.0146
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6303 Nucleic Acid Atoms Solvent Atoms 774 Heterogen Atoms 113
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing