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X-ray structure of TTR mutant - T119M at 1.22A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PVL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 2.1M di-sodium malonate
Crystal Properties Matthews coefficient Solvent content 2.29 46.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.91 α = 90 b = 85.721 β = 90 c = 63.359 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 PIXEL DECTRIS PILATUS 6M-F 2014-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97242 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.22 63.359 98.8 0.04 0.046 0.021 15.9 4.9 69325 69325
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.22 1.29 96 1.109 1.109 0.552 0.7 4.8 9704
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4PVL 1.22 38.37 65809 3482 98.54 0.1637 0.162 0.1706 0.1971 0.2046 RANDOM 23.614
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] 0.14 -0.11 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.119 r_sphericity_bonded 19.045 r_dihedral_angle_3_deg 13.21 r_rigid_bond_restr 10.892 r_dihedral_angle_4_deg 8.638 r_dihedral_angle_1_deg 6.498 r_mcangle_it 4.112 r_mcbond_other 3.796 r_mcbond_it 3.777 r_angle_refined_deg 1.972
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.119 r_sphericity_bonded 19.045 r_dihedral_angle_3_deg 13.21 r_rigid_bond_restr 10.892 r_dihedral_angle_4_deg 8.638 r_dihedral_angle_1_deg 6.498 r_mcangle_it 4.112 r_mcbond_other 3.796 r_mcbond_it 3.777 r_angle_refined_deg 1.972 r_angle_other_deg 1.884 r_chiral_restr 0.132 r_bond_refined_d 0.023 r_gen_planes_refined 0.011 r_gen_planes_other 0.01 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1794 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection XDS data reduction SCALA data scaling Coot model building MOLREP phasing