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Crystal structure of human Transthyretin (TTR) at pH 4.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BMZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 289 TTR pH 4.0 crystals were grown in the presence of 0.1 M sodium acetate (pH 4.0), 100 mM KCl, 1 mM EDTA and 0.3-0.5 M ammonium sulfate which was equilibrated against 2 M ammonium sulfate in hanging drop, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.1 41.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.224 α = 90 b = 85.082 β = 90 c = 62.92 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 120 IMAGE PLATE MAC Science DIP-2030 mirrors 2003-01-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.541
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.72 22.19 99.68 25276 25276
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.72 1.76 97.1
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 1BMZ 1.72 22.19 25276 25276 1290 99.68 0.22276 0.22276 0.22129 0.2291 0.24943 0.255 RANDOM 24.27
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 -0.04 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.224 r_dihedral_angle_4_deg 15.869 r_dihedral_angle_3_deg 13.35 r_dihedral_angle_1_deg 11.003 r_scangle_it 2.68 r_scbond_it 1.78 r_angle_refined_deg 1.353 r_mcangle_it 1.198 r_mcbond_it 1.094 r_angle_other_deg 0.854
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.224 r_dihedral_angle_4_deg 15.869 r_dihedral_angle_3_deg 13.35 r_dihedral_angle_1_deg 11.003 r_scangle_it 2.68 r_scbond_it 1.78 r_angle_refined_deg 1.353 r_mcangle_it 1.198 r_mcbond_it 1.094 r_angle_other_deg 0.854 r_symmetry_vdw_other 0.242 r_symmetry_vdw_refined 0.212 r_nbd_other 0.194 r_nbd_refined 0.179 r_nbtor_refined 0.174 r_mcbond_other 0.147 r_symmetry_hbond_refined 0.114 r_xyhbond_nbd_refined 0.097 r_chiral_restr 0.095 r_nbtor_other 0.084 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1754 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection DENZO data reduction SCALEPACK data scaling EPMR phasing