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Human Transthyretin expressed in Vibrio natriegens
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other In-house E. coli TTR structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 291.15 11.6 mg/mL protein in PBS pH 7.4 mixed 1:1 with MgFormate 0.1 M, 24 % PEG1000.
Crystal Properties Matthews coefficient Solvent content 2.06 40.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.439 α = 90 b = 62.896 β = 90 c = 85.593 γ = 90
Symmetry Space Group P 21 2 21
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 2021-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.979499 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.55 50.683 99 0.045 0.048 0.019 1 21.7 11.5 33691 20.267
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 8.49 89.3 0.605 0.751 0.437 0.772 1.4 5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE In-house E. coli TTR structure 1.55 50.683 33632 1666 98.848 0.184 0.1819 0.1858 0.227 0.2277 23.007
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] 1.95 -0.461 -1.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.538 r_dihedral_angle_4_deg 14.417 r_dihedral_angle_3_deg 11.05 r_rigid_bond_restr 7.864 r_dihedral_angle_1_deg 6.152 r_angle_other_deg 2.53 r_lrange_it 2.383 r_lrange_other 2.277 r_scangle_it 2.265 r_scangle_other 2.261
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.538 r_dihedral_angle_4_deg 14.417 r_dihedral_angle_3_deg 11.05 r_rigid_bond_restr 7.864 r_dihedral_angle_1_deg 6.152 r_angle_other_deg 2.53 r_lrange_it 2.383 r_lrange_other 2.277 r_scangle_it 2.265 r_scangle_other 2.261 r_scbond_other 2.176 r_scbond_it 2.174 r_angle_refined_deg 1.985 r_mcangle_it 1.858 r_mcangle_other 1.858 r_mcbond_it 1.706 r_mcbond_other 1.703 r_symmetry_nbd_refined 0.252 r_symmetry_nbd_other 0.218 r_symmetry_xyhbond_nbd_refined 0.188 r_nbd_refined 0.187 r_nbtor_refined 0.18 r_nbd_other 0.173 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.114 r_ncsr_local_group_1 0.112 r_symmetry_nbtor_other 0.089 r_symmetry_xyhbond_nbd_other 0.061 r_bond_other_d 0.037 r_gen_planes_other 0.023 r_bond_refined_d 0.018 r_gen_planes_refined 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1666 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing