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Crystal Structure of Sea Bream Transthyretin at 1.90A Resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F41 Human transthyretin, pdb code 1F41
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 296 PEG 1550 MME, sodium citrate, ammonium sulphate, nickel sulphate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.14 42.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.497 α = 90 b = 58.497 β = 90 c = 140.71 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 EMBL/DESY, HAMBURG X11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.75 50 97.1 0.047 46104
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.81 92.2 0.451
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Human transthyretin, pdb code 1F41 1.75 19.84 46104 39742 4439 100 0.1783 0.17836 0.17489 0.1951 0.20964 RANDOM 21.58
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] -0.18 -0.18 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.389 r_dihedral_angle_1_deg 3.959 r_scangle_it 2.757 r_scbond_it 1.622 r_mcangle_it 1.316 r_angle_refined_deg 1.303 r_angle_other_deg 0.718 r_mcbond_it 0.695 r_symmetry_vdw_refined 0.326 r_symmetry_vdw_other 0.278
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.389 r_dihedral_angle_1_deg 3.959 r_scangle_it 2.757 r_scbond_it 1.622 r_mcangle_it 1.316 r_angle_refined_deg 1.303 r_angle_other_deg 0.718 r_mcbond_it 0.695 r_symmetry_vdw_refined 0.326 r_symmetry_vdw_other 0.278 r_symmetry_hbond_refined 0.259 r_nbd_refined 0.228 r_nbd_other 0.215 r_xyhbond_nbd_refined 0.184 r_chiral_restr 0.082 r_xyhbond_nbd_other 0.049 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_nbtor_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_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 3529 Nucleic Acid Atoms Solvent Atoms 361 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CNS phasing