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Human transthyretin (TTR) complexed with diflunisal analogues- TTR. 2',6'-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 7 293 AMMONIUM SULFATE, 100 MM KCL, 1 MM EDTA, 10 MM SODIUM PHOSPHATE, SOAKED WITH THE INHIBITOR, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.16 43.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.236 α = 90 b = 85.139 β = 90 c = 64.768 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 120 CCD CCD-PXL-L600 2003-01-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 1.6 64.9 99.7 0.085 30717 30717
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.6 1.67 99.87
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 (All) 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 1.6 64.5 30717 30717 1624 99.68 0.23415 0.23415 0.23319 0.25191 RANDOM 21.587
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] -0.1 -0.05 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.421 r_dihedral_angle_3_deg 15.227 r_dihedral_angle_4_deg 13.336 r_dihedral_angle_1_deg 5.556 r_scangle_it 2.785 r_scbond_it 1.968 r_mcangle_it 1.352 r_angle_refined_deg 1.241 r_mcbond_it 1.198 r_angle_other_deg 0.689
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.421 r_dihedral_angle_3_deg 15.227 r_dihedral_angle_4_deg 13.336 r_dihedral_angle_1_deg 5.556 r_scangle_it 2.785 r_scbond_it 1.968 r_mcangle_it 1.352 r_angle_refined_deg 1.241 r_mcbond_it 1.198 r_angle_other_deg 0.689 r_symmetry_vdw_refined 0.252 r_symmetry_vdw_other 0.195 r_nbd_refined 0.185 r_nbd_other 0.184 r_nbtor_refined 0.178 r_mcbond_other 0.155 r_symmetry_hbond_refined 0.124 r_xyhbond_nbd_refined 0.121 r_nbtor_other 0.081 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1757 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 34
Software Software Software Name Purpose SAINT data scaling LSCALE data reduction AMoRE phasing REFMAC refinement SAINT data reduction LSCALE data scaling