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Crystal structure of human transthyretin in complex with 1-anilino-8-naphthalene sulfonate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CFM PDB ENTRY 3CFM
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 consisting of 1 uL mother liquor and 1 uL wtTTR 10 mg/mL; crystals appeared in about 5 days; complex obtained by soaking in mother liquor supplemented with saturating amount of ligand., VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.36 47.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.296 α = 90 b = 86.497 β = 90 c = 63.463 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 2005-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU ULTRAX 18 1.5418
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 1.87 51.168 93.5 0.043 0.043 13 7.2 19713 19329 2 2 17.7
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 1.87 1.96 79.8 0.184 0.184 4.1 6.9 2361
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 3CFM 1.87 26.25 19713 19297 994 94.87 0.203 0.203 0.2 0.1993 0.245 0.2432 RANDOM 17.107
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] -0.04 0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.38 r_dihedral_angle_4_deg 14.584 r_dihedral_angle_3_deg 13.654 r_dihedral_angle_1_deg 5.657 r_scangle_it 1.522 r_angle_refined_deg 1.08 r_scbond_it 0.985 r_mcangle_it 0.862 r_mcbond_it 0.481 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.38 r_dihedral_angle_4_deg 14.584 r_dihedral_angle_3_deg 13.654 r_dihedral_angle_1_deg 5.657 r_scangle_it 1.522 r_angle_refined_deg 1.08 r_scbond_it 0.985 r_mcangle_it 0.862 r_mcbond_it 0.481 r_nbtor_refined 0.305 r_nbd_refined 0.195 r_symmetry_vdw_refined 0.183 r_symmetry_hbond_refined 0.131 r_xyhbond_nbd_refined 0.123 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1778 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 42
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection