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Transthyretin in complex with a covalent small molecule kinetic stabilizer
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 The WT-TTR was concentrated to 4 mg/mL in 10 mM NaPi, 100 mM KCl, at pH 7.6 and co-crystallized at room temperature using the vapor diffusion sitting drop method. Crystals were grown from 1.395 M sodium citrate, 3.5% v/v glycerol at pH 5.5. The crystals were frozen using a cryo-protectant solution of 1.395 M sodium citrate, pH 5.5, containing 10% v/v glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.24 45.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.654 α = 90 b = 85.459 β = 90 c = 63.971 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 CCD MARMOSAIC 300 mm CCD 2008-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.003 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.34 38.17 98.1 0.049 33 7.1 52436
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.34 1.39 86.4 0.249 7.9 6.6
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 1.34 38.17 49727 2668 99.3 0.14881 0.14715 0.1565 0.18161 0.1887 RANDOM 13.041
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] 0.09 -0.24 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.359 r_dihedral_angle_4_deg 19.67 r_dihedral_angle_3_deg 13.516 r_sphericity_free 8.216 r_dihedral_angle_1_deg 6.268 r_scangle_it 5.405 r_sphericity_bonded 4.208 r_scbond_it 3.707 r_mcangle_it 2.886 r_rigid_bond_restr 2.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.359 r_dihedral_angle_4_deg 19.67 r_dihedral_angle_3_deg 13.516 r_sphericity_free 8.216 r_dihedral_angle_1_deg 6.268 r_scangle_it 5.405 r_sphericity_bonded 4.208 r_scbond_it 3.707 r_mcangle_it 2.886 r_rigid_bond_restr 2.126 r_mcbond_it 1.817 r_angle_refined_deg 1.629 r_angle_other_deg 1.352 r_mcbond_other 0.826 r_chiral_restr 0.099 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_gen_planes_other 0.008 r_bond_other_d 0.001 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1789 Nucleic Acid Atoms Solvent Atoms 234 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing