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Crystal structure of Cys10 sulfonated transthyretin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F86 PDB ENTRY 1F86
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 287 0.2M sodium acetate, 2.0 M ammonium sulphate, 6 % glycerol, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Crystal Properties Matthews coefficient Solvent content 2.08 40.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.331 α = 90 b = 85.945 β = 90 c = 63.404 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 CCD MARRESEARCH 2005-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9786 ESRF ID14-4
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 1.45 63.4 99.9 0.054 28.5 9.5 39635 39607 2
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 1.45 1.53 100 0.303 5.9 6.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 1F86 1.45 63.37 39635 39607 2104 99.93 0.18365 0.18289 0.1834 0.19818 0.1989 RANDOM 16.277
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] 0.22 -0.45 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.697 r_dihedral_angle_3_deg 11.056 r_dihedral_angle_4_deg 10.189 r_dihedral_angle_1_deg 5.801 r_scangle_it 2.903 r_scbond_it 1.972 r_mcangle_it 1.368 r_angle_refined_deg 1.22 r_mcbond_it 0.824 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.697 r_dihedral_angle_3_deg 11.056 r_dihedral_angle_4_deg 10.189 r_dihedral_angle_1_deg 5.801 r_scangle_it 2.903 r_scbond_it 1.972 r_mcangle_it 1.368 r_angle_refined_deg 1.22 r_mcbond_it 0.824 r_nbtor_refined 0.31 r_nbd_refined 0.192 r_symmetry_vdw_refined 0.17 r_symmetry_hbond_refined 0.112 r_xyhbond_nbd_refined 0.105 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1786 Nucleic Acid Atoms Solvent Atoms 221 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling PHASER phasing