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Human transthyretin (TTR) complexed with diflunisal analogues- TTR.3',5'-difluorobiphenyl-4-carboxylic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BMZ PDB ENTRY 1BMZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 ammonium sulfate, 100 mM KCL, 1 mM EDTA, 10 mM sodium phosphate, soaked with the inhibitor, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.15 42.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.935 α = 90 b = 84.852 β = 90 c = 63.742 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 CCD-PXL-L600 2002-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-D 1.0 APS 14-BM-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.54 42.18 95 0.03 33741 33741
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.54 1.6 98
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1BMZ 1.54 42.18 33741 33720 1693 95.7 0.23099 0.22234 0.24593 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.202 r_dihedral_angle_3_deg 15.82 r_dihedral_angle_4_deg 15.3 r_dihedral_angle_1_deg 6.68 r_scangle_it 4.113 r_scbond_it 2.829 r_angle_refined_deg 2.724 r_mcangle_it 2.014 r_mcbond_it 1.265 r_nbtor_refined 0.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.202 r_dihedral_angle_3_deg 15.82 r_dihedral_angle_4_deg 15.3 r_dihedral_angle_1_deg 6.68 r_scangle_it 4.113 r_scbond_it 2.829 r_angle_refined_deg 2.724 r_mcangle_it 2.014 r_mcbond_it 1.265 r_nbtor_refined 0.319 r_symmetry_hbond_refined 0.264 r_symmetry_vdw_refined 0.248 r_nbd_refined 0.238 r_xyhbond_nbd_refined 0.184 r_chiral_restr 0.123 r_bond_refined_d 0.067 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1718 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 34
Software Software Software Name Purpose AMoRE phasing REFMAC refinement XDS data reduction SCALEPACK data scaling