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Crystal structure of transthyretin in complex with iododiflunisal-betaAlaOMe
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 5.2 287 2.0 M ammonium sulfate, 7% glycerol and 0.2 M sodium acetate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Crystal Properties Matthews coefficient Solvent content 2.11 41.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.238 α = 90 b = 85.102 β = 90 c = 63.064 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 2005-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
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 1.85 563.12 99.8 0.056 32.4 9.5 18982 18945 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) 1.85 1.898 99.2 0.234 8.2 6.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1F86 1.85 63.12 18982 18982 1025 99.85 0.19945 0.19628 0.19553 0.1945 0.21019 0.2051 RANDOM 20.825
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 -0.87 0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.494 r_dihedral_angle_4_deg 21.462 r_dihedral_angle_3_deg 12.34 r_dihedral_angle_1_deg 5.357 r_scangle_it 4.532 r_scbond_it 2.887 r_mcangle_it 2.071 r_angle_refined_deg 1.608 r_mcbond_it 1.127 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.494 r_dihedral_angle_4_deg 21.462 r_dihedral_angle_3_deg 12.34 r_dihedral_angle_1_deg 5.357 r_scangle_it 4.532 r_scbond_it 2.887 r_mcangle_it 2.071 r_angle_refined_deg 1.608 r_mcbond_it 1.127 r_nbtor_refined 0.31 r_nbd_refined 0.211 r_symmetry_hbond_refined 0.193 r_symmetry_vdw_refined 0.191 r_xyhbond_nbd_refined 0.157 r_chiral_restr 0.099 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 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 1780 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 50
Software Software Software Name Purpose DNA data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling