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Crystal structure of human transthyretin variant A25T in complex with flufenamic acid.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3I9A PDB entry 3I9A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1 M Hepes sodium pH 7.5, 28% PEG 400, 0.2 calcium chloride dihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K, soaking for 1 h with ligand.
Crystal Properties Matthews coefficient Solvent content 2.22 44.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.93 α = 90 b = 85.607 β = 90 c = 65.228 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 MARMOSAIC 225 mm CCD 2008-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.4586 LNLS W01B-MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.9 65.233 98.6 0.057 0.057 17.5 4.6 19697 19697 24.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 97.6 0.31 0.31 2.4 4.6 2811
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3I9A 1.9 26.14 19685 1009 98.16 0.2011 0.1987 0.1986 0.2474 0.2477 RANDOM 24.2611
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 -0.85 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.694 r_dihedral_angle_4_deg 18.273 r_dihedral_angle_3_deg 15.72 r_dihedral_angle_1_deg 5.891 r_scangle_it 2.383 r_scbond_it 1.64 r_angle_refined_deg 1.368 r_mcangle_it 1.231 r_mcbond_it 0.712 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.694 r_dihedral_angle_4_deg 18.273 r_dihedral_angle_3_deg 15.72 r_dihedral_angle_1_deg 5.891 r_scangle_it 2.383 r_scbond_it 1.64 r_angle_refined_deg 1.368 r_mcangle_it 1.231 r_mcbond_it 0.712 r_nbtor_refined 0.298 r_symmetry_vdw_refined 0.238 r_nbd_refined 0.204 r_xyhbond_nbd_refined 0.146 r_symmetry_hbond_refined 0.134 r_chiral_restr 0.083 r_bond_refined_d 0.014 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1789 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 40
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection