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Crystal structure of human wild-type transthyretin in complex with diclofenac
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CFM PDB entry 3CFM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 mother liquor: 100 mM Tris, pH7.5, 100 mM KCl, 20 % v/v PEG400; drop: 1 uL mother liquor + 1 uL wtTTR 10 mg/mL; crystals appeared in 5 days; complexes obtained by soaking in mother liquor supplemented with saturating amount of diclofenac, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.26 45.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.07 α = 90 b = 85.49 β = 90 c = 63.62 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 IMAGE PLATE MAR scanner 345 mm plate Osmic 2005-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU ULTRAX 18 1.5418
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 2.09 85.49 94.7 0.074 0.074 9.2 4.1 13772 13634 2 2 23.8
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) 2.09 2.2 97.7 0.331 0.331 2.3 4 2018
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 3CFM 2.09 35.67 13772 13634 696 93.95 0.211 0.211 0.209 0.2062 0.249 0.2474 RANDOM 20.972
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] 0.11 -0.05 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.845 r_dihedral_angle_4_deg 17.673 r_dihedral_angle_3_deg 15.577 r_dihedral_angle_1_deg 6.514 r_angle_refined_deg 1.116 r_scangle_it 0.732 r_mcangle_it 0.725 r_scbond_it 0.42 r_mcbond_it 0.404 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.845 r_dihedral_angle_4_deg 17.673 r_dihedral_angle_3_deg 15.577 r_dihedral_angle_1_deg 6.514 r_angle_refined_deg 1.116 r_scangle_it 0.732 r_mcangle_it 0.725 r_scbond_it 0.42 r_mcbond_it 0.404 r_nbtor_refined 0.304 r_nbd_refined 0.191 r_symmetry_vdw_refined 0.188 r_symmetry_hbond_refined 0.115 r_xyhbond_nbd_refined 0.104 r_chiral_restr 0.074 r_bond_refined_d 0.006 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1957 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 38
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection