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Crystal structure of DACM wild type Transthyretin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GKO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.2 M CaCl2
0.1 M HEPES sodium pH 7.5
28% v/v PEG 400
Crystal Properties Matthews coefficient Solvent content 1.89 34.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.68 α = 90 b = 64.49 β = 90 c = 85.27 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 110 PIXEL DECTRIS PILATUS3 S 6M Toroidal mirror 2015-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.984003 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.42 22.35 99.3 0.097 8.1 5 45907
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.42 1.5 99.2 0.73 2.1 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 (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 1GKO 1.42 22.35 43621 2223 99.12 0.16231 0.15958 0.1603 0.21693 0.2188 RANDOM 23.389
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] 1.15 -0.67 -0.48
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 22.327 r_sphericity_bonded 15.573 r_rigid_bond_restr 6.372 r_scangle_other 5.649 r_long_range_B_refined 5.328 r_long_range_B_other 5.171 r_scbond_other 4.987 r_scbond_it 4.978 r_mcangle_other 3.7 r_mcangle_it 3.692
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 22.327 r_sphericity_bonded 15.573 r_rigid_bond_restr 6.372 r_scangle_other 5.649 r_long_range_B_refined 5.328 r_long_range_B_other 5.171 r_scbond_other 4.987 r_scbond_it 4.978 r_mcangle_other 3.7 r_mcangle_it 3.692 r_mcbond_it 3.002 r_mcbond_other 2.968 r_angle_refined_deg 1.683 r_angle_other_deg 0.846 r_chiral_restr 0.108 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1785 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing