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Transthyretin in complex with (E)-2,6-dibromo-4-(2,6-dichlorostyryl)phenol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QGB pdb entry 2QGB
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 298K
Crystal Properties Matthews coefficient Solvent content 2.14 42.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.927 α = 90 b = 85.002 β = 90 c = 64.506 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 325 mm CCD Flat collimating mirror, double crystal monochromator, toroid focusing mirror M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.9194 SSRL BL9-2
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 1.7 64.55 99.5 0.057 34.6 14 26903 23.6
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) 1.7 1.76 97 0.695 7.3 11.9 2588
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 2QGB 1.7 50 26562 1333 99.56 0.172 0.169 0.1775 0.217 0.2174 RANDOM 27.504
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] 1.18 -0.72 -0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.117 r_dihedral_angle_4_deg 17.51 r_dihedral_angle_3_deg 14.69 r_sphericity_free 10.749 r_dihedral_angle_1_deg 5.988 r_scangle_it 5.86 r_sphericity_bonded 5.544 r_rigid_bond_restr 5.136 r_scbond_it 4.646 r_mcangle_it 3.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.117 r_dihedral_angle_4_deg 17.51 r_dihedral_angle_3_deg 14.69 r_sphericity_free 10.749 r_dihedral_angle_1_deg 5.988 r_scangle_it 5.86 r_sphericity_bonded 5.544 r_rigid_bond_restr 5.136 r_scbond_it 4.646 r_mcangle_it 3.06 r_mcbond_it 2.563 r_angle_refined_deg 1.818 r_angle_other_deg 0.927 r_mcbond_other 0.921 r_nbd_other 0.203 r_nbd_refined 0.196 r_symmetry_vdw_refined 0.191 r_nbtor_refined 0.186 r_symmetry_hbond_refined 0.183 r_symmetry_vdw_other 0.168 r_xyhbond_nbd_refined 0.163 r_chiral_restr 0.109 r_nbtor_other 0.092 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1863 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing