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Rat transthyretin (also called prealbumin) complex with 3',5'-dibromoflavone (EMD21388)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GKE TETRAMER OF RAT TTR, PDB ENTRY 1GKE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 ammonium sulphate, acetate buffer, pH 5.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.46 46.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.545 α = 90 b = 82.545 β = 90 c = 161.741 γ = 90
Symmetry Space Group P 43 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 293 IMAGE PLATE RIGAKU RAXIS II COLLIMATOR M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 2.3 82.5 92.8 0.1023 5.9 4.86 23846 6.8
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) 2.3 2.4 81.1 0.367 2.1 2.57 886
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT TETRAMER OF RAT TTR, PDB ENTRY 1GKE 2.3 12 2.5 23613 16330 793 64.3 0.207 0.207 0.203 0.288 RANDOM 13.8
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] -0.1 -0.1 0.21
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.2 c_scbond_it 13.08 c_scangle_it 11.99 c_mcangle_it 2.72 c_mcbond_it 1.57 c_angle_deg 1.3 c_improper_angle_d 1.1 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3736 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 66
Software Software Software Name Purpose CNS refinement CNS phasing