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X-ray structure of TTR mutant - S52P at 1.23A 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 2.5M di-sodium malonate
Crystal Properties Matthews coefficient Solvent content 2.32 47.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.017 α = 90 b = 85.929 β = 90 c = 63.964 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 1.23 63.964 97.5 0.042 0.049 0.024 13.5 3.8 67662 67662
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 1.23 1.3 94.1 0.725 0.725 0.417 1.1 3.8 9390
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 1.23 35.7 64225 3409 97.18 0.1585 0.157 0.1615 0.1857 0.1813 RANDOM 25.514
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] 0.13 -0.01 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.172 r_sphericity_bonded 24.356 r_rigid_bond_restr 15.98 r_dihedral_angle_4_deg 14.817 r_dihedral_angle_3_deg 13.703 r_dihedral_angle_1_deg 6.403 r_mcangle_it 4.871 r_mcbond_it 4.763 r_mcbond_other 4.234 r_angle_other_deg 3.536
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.172 r_sphericity_bonded 24.356 r_rigid_bond_restr 15.98 r_dihedral_angle_4_deg 14.817 r_dihedral_angle_3_deg 13.703 r_dihedral_angle_1_deg 6.403 r_mcangle_it 4.871 r_mcbond_it 4.763 r_mcbond_other 4.234 r_angle_other_deg 3.536 r_angle_refined_deg 2.062 r_chiral_restr 0.134 r_bond_refined_d 0.023 r_gen_planes_other 0.02 r_gen_planes_refined 0.012 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1794 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection XDS data reduction SCALA data scaling Coot model building MOLREP phasing