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Human TTR altered conformation from soaking in CuCl2.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5K1J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 protein: 10 mg/ml Dialysed in 100 milli-M NaCl, 50 milli-M sodium acetate, pH 5.5 Precipitant: 21 % PEG4K, .14 M imidazole malate, pH 6.0, 3.6% MPEG 5K, 0.03 M sodium acetate, pH 5.5 cryosoak: 40% CM1 (12.5 % di-ethylene glycol + 12.5 % MPD + 37.5 % 1,2-propanediol + 12.5 % DMSO ), 25 % MPEG 5K,0.1 M CHC (citric acid, HEPES, CHES) 90 % acid at pH 4.0 / 10 % basic at pH 10.0), 30 min soak.
Crystal Properties Matthews coefficient Solvent content 2.37 48.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.99 α = 90 b = 82.54 β = 90 c = 67.77 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 EIGER X 9M mirrors 2016-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.980035 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 2.44 50 99.5 0.107 0.09 0.998 12.59 7.02 17252 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.44 2.59 96.7 0.672 0.621 0.912 3.29 6.84
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 5K1J 2.45 41.27 8868 467 99.97 0.17261 0.16853 0.1734 0.25386 0.2601 RANDOM 46.362
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] -1.36 -0.69 2.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.395 r_dihedral_angle_3_deg 17.701 r_dihedral_angle_4_deg 16.432 r_long_range_B_refined 12.175 r_long_range_B_other 12.172 r_scangle_other 8.168 r_dihedral_angle_1_deg 7.132 r_mcangle_other 6.326 r_mcangle_it 6.323 r_scbond_it 5.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.395 r_dihedral_angle_3_deg 17.701 r_dihedral_angle_4_deg 16.432 r_long_range_B_refined 12.175 r_long_range_B_other 12.172 r_scangle_other 8.168 r_dihedral_angle_1_deg 7.132 r_mcangle_other 6.326 r_mcangle_it 6.323 r_scbond_it 5.08 r_scbond_other 5.078 r_mcbond_it 4.071 r_mcbond_other 4.051 r_angle_refined_deg 1.714 r_angle_other_deg 0.97 r_chiral_restr 0.095 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1792 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing