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Crystal structure of human TTR mutant L111M bound to tafamidis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8AWW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1 M HEPES, 0.4 M CaCl2, 34% PEG400
Crystal Properties Matthews coefficient Solvent content 2.23 44.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.343 α = 90 b = 84.816 β = 90 c = 63.043 γ = 90
Symmetry Space Group P 21 21 2
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 Bruker PHOTON II 2025-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 VENTURE 1.541
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.7 42.44 95.5 0.1 0.99 9 5.5 24345
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.8 0.64 1.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.7 42.44 23131 1211 94.51 0.21677 0.21589 0.222 0.23302 0.2367 RANDOM 25.447
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] 0.75 -0.86 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.593 r_dihedral_angle_2_deg 10.606 r_long_range_B_refined 8.211 r_long_range_B_other 8.197 r_dihedral_angle_1_deg 6.854 r_scangle_other 5.25 r_mcangle_it 4.444 r_mcangle_other 4.442 r_scbond_it 3.324 r_scbond_other 3.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.593 r_dihedral_angle_2_deg 10.606 r_long_range_B_refined 8.211 r_long_range_B_other 8.197 r_dihedral_angle_1_deg 6.854 r_scangle_other 5.25 r_mcangle_it 4.444 r_mcangle_other 4.442 r_scbond_it 3.324 r_scbond_other 3.322 r_mcbond_it 2.713 r_mcbond_other 2.703 r_angle_refined_deg 1.747 r_angle_other_deg 0.586 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 1805 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling MOLREP phasing