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Crystal structure of the apo form of human wild-type transthyretin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F41 PDB ENTRY 1F41
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 Mother liquor: 100 mM tris pH 7.5, 100 mM KCl, 20 % v/v PEG 400; drop 1 uL mother liquor + 1 uL TTR 10 mg/mL; crystals appeared in about 5 days, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.33 47.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.169 α = 90 b = 86.109 β = 90 c = 63.764 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 Osmic 2005-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU ULTRAX 18 1.542
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 1.6 86.109 99.9 0.046 0.046 8.9 6.9 32087 32073 2 2 20.5
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) 1.6 1.69 100 0.398 0.398 1.9 6.7 4565
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1F41 1.6 17.87 32061 32042 1624 99.96 0.192 0.192 0.191 0.1867 0.218 0.2151 RANDOM 21.203
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] -0.02 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.885 r_dihedral_angle_4_deg 15.355 r_dihedral_angle_3_deg 13.435 r_dihedral_angle_1_deg 5.758 r_angle_refined_deg 1.057 r_nbtor_refined 0.301 r_nbd_refined 0.181 r_symmetry_vdw_refined 0.18 r_xyhbond_nbd_refined 0.119 r_symmetry_hbond_refined 0.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.885 r_dihedral_angle_4_deg 15.355 r_dihedral_angle_3_deg 13.435 r_dihedral_angle_1_deg 5.758 r_angle_refined_deg 1.057 r_nbtor_refined 0.301 r_nbd_refined 0.181 r_symmetry_vdw_refined 0.18 r_xyhbond_nbd_refined 0.119 r_symmetry_hbond_refined 0.103 r_chiral_restr 0.072 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1955 Nucleic Acid Atoms Solvent Atoms 282 Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection