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Crystal structure of the F87M/L110M mutant of human transthyretin at pH 7.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F41 PDB entry 1f41
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 ZINC ACETATE 0.2 M, SODIUM CITRATE 0.1 M, AMMONIUM SULFATE 2,0M, PH 7.5; CRYSTALS WERE SOAKED IN MOTHER LIQUOR SUPPLEMENTED WITH 10 % GLYCEROL BEFORE FREEZING IN LIQUID NITROGEN, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.21 44.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.325 α = 90 b = 61.925 β = 89.93 c = 47.3 γ = 90
Symmetry Space Group P 1 21 1
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 2008-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.458 LNLS W01B-MX2
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 1.9 24.72 99.9 0.063 13.7 3.7 41141 28.724
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) 1.9 1.95 100 0.394 2.7 3.6 5965
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 1f41 1.9 24.72 36135 1892 99.81 0.19383 0.19063 0.1944 0.25496 0.2555 RANDOM 35.289
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] -0.42 -0.16 0.96 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.835 r_dihedral_angle_3_deg 18.686 r_dihedral_angle_4_deg 14.481 r_dihedral_angle_1_deg 7.569 r_sphericity_free 7.339 r_scangle_it 4.963 r_sphericity_bonded 4.464 r_scbond_it 3.24 r_mcangle_it 2.532 r_rigid_bond_restr 2.068
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.835 r_dihedral_angle_3_deg 18.686 r_dihedral_angle_4_deg 14.481 r_dihedral_angle_1_deg 7.569 r_sphericity_free 7.339 r_scangle_it 4.963 r_sphericity_bonded 4.464 r_scbond_it 3.24 r_mcangle_it 2.532 r_rigid_bond_restr 2.068 r_angle_refined_deg 1.899 r_mcbond_it 1.523 r_chiral_restr 0.149 r_bond_refined_d 0.018 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3551 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms 64
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling