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Human TTR altered conformation from soaking in iron chloride.
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: 27 % polyethylene glycol 4,000, 0.2 M imidazole malate, pH 6.0. cryosoak: 40%
SM3 (, 25 % MPEG 5K, 25 %
diethylene glycol + 25 % ethylene glycol + 25 % glycerol + 25 % 1,4-dioxane) 25 % MPEG 5K,
0.1 M CHC (citric acid, HEPES, CHES: 90 % acid /10 % basic), 30 mM FeCl2, 2 h soak.
Crystal Properties Matthews coefficient Solvent content 2.39 48.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.73 α = 90 b = 81.81 β = 90 c = 69.46 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 2016-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 1.73915 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 2.53 50 99.2 0.2 0.185 0.996 8.28 13.21 15593 -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 2.53 2.68 95.3 1.98 1.82 0.3 0.83 12.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5K1J 2.53 40.9 8113 427 99.45 0.19508 0.19205 0.25252 0.2381 RANDOM 52.976
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] -1.07 1.74 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.473 r_dihedral_angle_4_deg 18.591 r_dihedral_angle_3_deg 16.948 r_long_range_B_other 12.248 r_long_range_B_refined 12.223 r_scangle_other 8.559 r_dihedral_angle_1_deg 6.963 r_mcangle_it 6.268 r_mcangle_other 6.266 r_scbond_it 5.657
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.473 r_dihedral_angle_4_deg 18.591 r_dihedral_angle_3_deg 16.948 r_long_range_B_other 12.248 r_long_range_B_refined 12.223 r_scangle_other 8.559 r_dihedral_angle_1_deg 6.963 r_mcangle_it 6.268 r_mcangle_other 6.266 r_scbond_it 5.657 r_scbond_other 5.654 r_mcbond_it 3.852 r_mcbond_other 3.851 r_angle_refined_deg 1.604 r_angle_other_deg 0.932 r_chiral_restr 0.088 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 101 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing