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X-ray structure of perdeuterated wild-type TTR at 1.42A 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 5.5 298 2.4M di-sodium malonate
Crystal Properties Matthews coefficient Solvent content 2.31 46.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.64 α = 90 b = 85.793 β = 90 c = 64.158 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 1.419 64.158 99.5 0.043 0.049 0.023 15.6 4.3 45102 45102
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 1.42 1.5 98.6 1.392 1.392 0.732 0.5 4.3 6427
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 1.42 64.158 42792 2268 99.4 0.154 0.1518 0.1604 0.1984 0.2021 RANDOM 29.133
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] -0.64 0.41 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.748 r_sphericity_bonded 20.769 r_dihedral_angle_4_deg 16.857 r_dihedral_angle_3_deg 13.934 r_rigid_bond_restr 9.46 r_dihedral_angle_1_deg 5.998 r_mcangle_it 4.174 r_mcbond_it 4.151 r_mcbond_other 4.123 r_angle_refined_deg 1.777
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.748 r_sphericity_bonded 20.769 r_dihedral_angle_4_deg 16.857 r_dihedral_angle_3_deg 13.934 r_rigid_bond_restr 9.46 r_dihedral_angle_1_deg 5.998 r_mcangle_it 4.174 r_mcbond_it 4.151 r_mcbond_other 4.123 r_angle_refined_deg 1.777 r_angle_other_deg 0.92 r_chiral_restr 0.117 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1792 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms
Software Software Software Name Purpose MxCuBE data collection XDS data reduction SCALA data scaling MOLREP phasing REFMAC refinement Coot model building