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Human transthyretin (TTR) in complex with N-(3,5-Dibromo-4-hydroxyphenyl)benzamide
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 2.12 41.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.605 α = 90 b = 85.23 β = 90 c = 64.322 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 CCD MARMOSAIC 325 mm CCD 2007-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.9795 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 1.4 50 96.9 0.033 39.8 7 45445 20.7
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) 1.4 1.45 89.8 0.426 3.5 5.5
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 1.4 32.79 45410 2292 96.97 0.175 0.174 0.1786 0.202 0.2076 RANDOM 17.017
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] -0.45 0.52 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.922 r_dihedral_angle_4_deg 19.33 r_dihedral_angle_3_deg 13.849 r_sphericity_free 11.367 r_sphericity_bonded 6.796 r_dihedral_angle_1_deg 5.919 r_scangle_it 5.527 r_scbond_it 4.363 r_mcangle_it 3.102 r_mcbond_it 2.573
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.922 r_dihedral_angle_4_deg 19.33 r_dihedral_angle_3_deg 13.849 r_sphericity_free 11.367 r_sphericity_bonded 6.796 r_dihedral_angle_1_deg 5.919 r_scangle_it 5.527 r_scbond_it 4.363 r_mcangle_it 3.102 r_mcbond_it 2.573 r_rigid_bond_restr 2.21 r_angle_refined_deg 1.792 r_mcbond_other 1.148 r_angle_other_deg 0.957 r_nbd_refined 0.218 r_nbd_other 0.207 r_symmetry_vdw_other 0.207 r_nbtor_refined 0.186 r_symmetry_vdw_refined 0.184 r_xyhbond_nbd_refined 0.12 r_chiral_restr 0.118 r_symmetry_hbond_refined 0.094 r_nbtor_other 0.09 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1891 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing