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Human transthyretin (TTR) complexed with (2,7-Dichloro-fluoren-9-ylideneaminooxy)-acetic acid.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4TQ8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 Protein: TTR at 5 mg/ml + 1.6 milli-M inhibitor.
Precipitant: 18% PEG4K, 0.08M imidazole
malate, pH 6.0 and 13.5% PEG10K, 0.06M ammonium acetate, pH 4.5
Cryoprotectant: 10% diethylene glycol + 5% MPD + 15% 2,3-butanediol + 5% 1,4-dioxane, 25% MPEG 5K, 0.1 M mixed (Na acetate, ADA, Bicine - 60% at pH 4/40% at pH 10)
1 milli-M inhibitor.
Crystal Properties Matthews coefficient Solvent content 2.01 38.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.21 α = 90 b = 85.99 β = 90 c = 63.82 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 DECTRIS PILATUS 6M-F mirrors 2014-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.87006 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.33 43.21 99.9 0.076 0.072 14.92 9.12 55430 55377 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.33 1.36 99.9 1.86 1.22 9.23
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 4TQ8 1.33 42.99 52608 2769 99.9 0.14202 0.13944 0.1401 0.19239 0.1931 RANDOM 24.215
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] -0.69 0.31 0.38
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 45.611 r_dihedral_angle_2_deg 30.932 r_sphericity_bonded 18.658 r_dihedral_angle_4_deg 15.784 r_dihedral_angle_3_deg 15.012 r_rigid_bond_restr 7.789 r_dihedral_angle_1_deg 6.624 r_long_range_B_refined 6.244 r_scbond_it 4.285 r_mcangle_it 3.625
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 45.611 r_dihedral_angle_2_deg 30.932 r_sphericity_bonded 18.658 r_dihedral_angle_4_deg 15.784 r_dihedral_angle_3_deg 15.012 r_rigid_bond_restr 7.789 r_dihedral_angle_1_deg 6.624 r_long_range_B_refined 6.244 r_scbond_it 4.285 r_mcangle_it 3.625 r_mcbond_it 2.867 r_angle_refined_deg 2.452 r_chiral_restr 0.188 r_bond_refined_d 0.028 r_gen_planes_refined 0.015 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1793 Nucleic Acid Atoms Solvent Atoms 267 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing Coot model building