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Structure of full-length amyloidogenic immunoglobulin light chain H9 in complex with (E)-3-nitro-4-(2-(2-phenylpropylidene)hydrazineyl)benzenesulfonamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5M6A PDB entry 5M6A
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 2.69 54.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.141 α = 106.31 b = 95.655 β = 92.93 c = 125.918 γ = 90.16
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 2021-04-16 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 Sym I (Observed) 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 47.58 96.4 0.086 0.054 1 8.7 3.5 182621 22
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 95 0.381 0.241 0.87 3.4 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 5M6A 2 47.62 173255 9361 96.41 0.23174 0.22909 0.2347 0.28009 0.2841 RANDOM 32.175
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] -1.08 0.03 -0.47 -1.95 0.62 2.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.375 r_dihedral_angle_4_deg 17.465 r_dihedral_angle_3_deg 14.817 r_dihedral_angle_1_deg 8.075 r_long_range_B_refined 6.755 r_long_range_B_other 6.702 r_mcangle_it 4.088 r_mcangle_other 4.088 r_scangle_other 4.067 r_mcbond_it 2.683
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.375 r_dihedral_angle_4_deg 17.465 r_dihedral_angle_3_deg 14.817 r_dihedral_angle_1_deg 8.075 r_long_range_B_refined 6.755 r_long_range_B_other 6.702 r_mcangle_it 4.088 r_mcangle_other 4.088 r_scangle_other 4.067 r_mcbond_it 2.683 r_mcbond_other 2.683 r_scbond_it 2.628 r_scbond_other 2.618 r_angle_other_deg 2.449 r_angle_refined_deg 1.555 r_chiral_restr 0.065 r_bond_other_d 0.037 r_gen_planes_other 0.009 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18744 Nucleic Acid Atoms Solvent Atoms 1390 Heterogen Atoms 174
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing