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Human transthyretin (TTR) complexed with (R)-3-(9H-fluoren-9-ylideneaminooxy)-2-methyl-N-(methylsulfonyl) propionamide in a dual binding mode
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4TQI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.7 293 Protein: 5 mg/ml in 0.05 M NaCl, 0.05 M sodium acetate, pH 5.5.
Precipitant: 60% (30% PEG-4K, 0.2 M imidazole malate, pH 6.0) and 40% (MPEG-5K, 0.1 M sodium acetate, pH 5.5).
Cryoprotectant: 40% (25 % diethylene glycol, 12.5 % MPD, 37.5 % 2,3-butanediol, 12.5 % 1,4-dioxane), 12.5% MPEG 5K, 25% MPEG 550, 0.1 M (sodium propionate, sodium cacodylate, Bis-Tris-propane: 50% component A pH 4; 50% B pH 9.5) with 1 milli-M ligand.
Crystal Properties Matthews coefficient Solvent content 2.14 42.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.121 α = 90 b = 86.081 β = 90 c = 63.473 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 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 1.58 51.1 99.9 0.125 0.118 14.12 9.19 33125 33100 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.58 1.64 99.9 1.87 9.5
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 4TQI 1.58 51.09 31425 1674 99.92 0.14441 0.14148 0.1385 0.19761 0.1961 RANDOM 19.98
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] 0.19 -0.21 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.429 r_dihedral_angle_4_deg 18.643 r_dihedral_angle_3_deg 14.398 r_scangle_it 7.776 r_dihedral_angle_1_deg 6.799 r_scbond_it 5.449 r_mcangle_it 4.253 r_rigid_bond_restr 2.867 r_mcbond_it 2.728 r_angle_refined_deg 2.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.429 r_dihedral_angle_4_deg 18.643 r_dihedral_angle_3_deg 14.398 r_scangle_it 7.776 r_dihedral_angle_1_deg 6.799 r_scbond_it 5.449 r_mcangle_it 4.253 r_rigid_bond_restr 2.867 r_mcbond_it 2.728 r_angle_refined_deg 2.15 r_chiral_restr 0.157 r_bond_refined_d 0.023 r_gen_planes_refined 0.011 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_other r_long_range_B_refined r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1792 Nucleic Acid Atoms Solvent Atoms 260 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement Coot model building XDS data scaling XSCALE data scaling ADSC data collection