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Crystal structure of I73L mutated human transthyretin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4N85
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 293 24% PEG400, 0.2 M magnesium acetate, 5% glycerol, 0.1 M Tris-HCl
Crystal Properties Matthews coefficient Solvent content 1.97 37.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.8398 α = 90 b = 85.84 β = 90 c = 64.16 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 CCD RAYONIX MX225HE 2017-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.000 SPring-8 BL26B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.418 35.7 99.7 0.085 0.092 0.035 0.996 13.3 7 45459 15.4395742663
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.418 1.49 0.471 0.512 0.197 0.898 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4N85 1.41800705321 35.6739160745 1.343194049 45459 2245 99.5728742279 0.185636914987 0.184394332498 0.186 0.210395487158 0.2106 23.7283313261
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.6400886742 f_angle_d 1.04801539985 f_chiral_restr 0.0405769339793 f_bond_d 0.00742798941176 f_plane_restr 0.00702329798019
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1766 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction SCALA data scaling PHASER phasing