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X-ray structure of perdeuterated TTR mutant - S52P at 1.28A 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 2.1M di-sodium malonate
Crystal Properties Matthews coefficient Solvent content 2.31 46.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.774 α = 90 b = 85.802 β = 90 c = 64.153 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 1.28 64.153 99.7 0.064 0.072 0.032 11 4.9 61400 61400
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 1.28 1.35 99.6 1.076 1.076 0.531 0.7 4.9 8809
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 1.28 42.9 58244 3106 99.65 0.1509 0.1495 0.1594 0.1758 0.1831 RANDOM 24.203
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] -0.18 0.35 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.088 r_sphericity_bonded 20.533 r_dihedral_angle_3_deg 14.909 r_rigid_bond_restr 14.564 r_dihedral_angle_4_deg 12.389 r_dihedral_angle_1_deg 6.299 r_mcangle_it 4.509 r_mcbond_it 4.287 r_mcbond_other 4.267 r_angle_refined_deg 2.052
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.088 r_sphericity_bonded 20.533 r_dihedral_angle_3_deg 14.909 r_rigid_bond_restr 14.564 r_dihedral_angle_4_deg 12.389 r_dihedral_angle_1_deg 6.299 r_mcangle_it 4.509 r_mcbond_it 4.287 r_mcbond_other 4.267 r_angle_refined_deg 2.052 r_angle_other_deg 1.173 r_chiral_restr 0.132 r_bond_refined_d 0.022 r_gen_planes_refined 0.012 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1794 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 12
Software Software Software Name Purpose MxCuBE data collection XDS data reduction SCALA data scaling REFMAC refinement Coot model building MOLREP phasing