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Crystal structure of human transthyretin variant A25T in complex with thyroxine (T4)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1M Hepes sodium pH 7.5, 28% PEG 400, 0.2 calcium chloride dihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K, complex obtained by soaking crystal with ligand.
Crystal Properties Matthews coefficient Solvent content 2.14 42.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.13 α = 90 b = 85.31 β = 90 c = 64.34 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 IMAGE PLATE MAR scanner 345 mm plate 2008-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.4586 LNLS W01B-MX2
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 1.9 64.34 99.8 0.061 0.061 17.6 4.1 19350 19350 23.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 100 0.26 0.26 2.8 4.1
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 THROUGHOUT 1.9 26.01 18174 1146 99.8 0.191 0.188 0.1919 0.236 0.2343 RANDOM 26.16
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] 2.51 -1.42 -1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.842 r_dihedral_angle_4_deg 17.135 r_dihedral_angle_3_deg 16.489 r_dihedral_angle_1_deg 6.834 r_scangle_it 4.818 r_scbond_it 2.988 r_mcangle_it 2.035 r_angle_refined_deg 1.823 r_mcbond_it 1.125 r_chiral_restr 0.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.842 r_dihedral_angle_4_deg 17.135 r_dihedral_angle_3_deg 16.489 r_dihedral_angle_1_deg 6.834 r_scangle_it 4.818 r_scbond_it 2.988 r_mcangle_it 2.035 r_angle_refined_deg 1.823 r_mcbond_it 1.125 r_chiral_restr 0.127 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1789 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 48
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection REFMAC phasing