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X-ray structure of perdeuterated TTR mutant - T119M at 1.22A
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, SITTING DROP 5.5 298 2.4M di-sodium malonate
Crystal Properties Matthews coefficient Solvent content 2.31 46.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.006 α = 90 b = 85.617 β = 90 c = 63.943 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 63.943 99.7 0.04 0.046 0.022 18.3 4.2 70831 70831
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 99 0.601 0.601 0.332 1.3 4 10138
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 42.81 67206 3577 99.63 0.1649 0.1632 0.1663 0.196 0.1949 RANDOM 22.637
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] -0.15 0.07 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.912 r_sphericity_bonded 17.802 r_dihedral_angle_3_deg 12.784 r_rigid_bond_restr 10.57 r_dihedral_angle_4_deg 9.747 r_dihedral_angle_1_deg 6.25 r_mcangle_it 3.851 r_mcbond_it 3.646 r_mcbond_other 3.638 r_angle_refined_deg 2.155
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.912 r_sphericity_bonded 17.802 r_dihedral_angle_3_deg 12.784 r_rigid_bond_restr 10.57 r_dihedral_angle_4_deg 9.747 r_dihedral_angle_1_deg 6.25 r_mcangle_it 3.851 r_mcbond_it 3.646 r_mcbond_other 3.638 r_angle_refined_deg 2.155 r_angle_other_deg 1.925 r_chiral_restr 0.132 r_bond_refined_d 0.024 r_gen_planes_refined 0.012 r_gen_planes_other 0.01 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1794 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection XDS data reduction SCALA data scaling Coot model building MOLREP phasing