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X-ray structure of wild-type TTR at 1.30A 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 5 298 2.15M di-sodium malonate
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.751 α = 90 b = 85.486 β = 90 c = 64.538 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 1.299 64.538 99.6 0.032 0.037 0.017 15.8 4.2 58869 58869
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 1.3 1.37 98.1 0.94 0.94 0.519 0.8 4.2 8349
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 1.3 51.51 55840 2981 99.54 0.154 0.1525 0.1525 0.1801 0.1815 RANDOM 26.947
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] -0.59 0.16 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.93 r_dihedral_angle_4_deg 24.286 r_sphericity_bonded 20.747 r_dihedral_angle_3_deg 13.68 r_rigid_bond_restr 10.576 r_dihedral_angle_1_deg 6.121 r_mcangle_it 4.457 r_mcbond_it 3.712 r_mcbond_other 3.691 r_angle_refined_deg 1.985
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.93 r_dihedral_angle_4_deg 24.286 r_sphericity_bonded 20.747 r_dihedral_angle_3_deg 13.68 r_rigid_bond_restr 10.576 r_dihedral_angle_1_deg 6.121 r_mcangle_it 4.457 r_mcbond_it 3.712 r_mcbond_other 3.691 r_angle_refined_deg 1.985 r_angle_other_deg 1.035 r_chiral_restr 0.134 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1792 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms
Software Software Software Name Purpose MxCuBE data collection XDS data reduction SCALA data scaling MOLREP phasing REFMAC refinement Coot model building