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Crystal structure of the F87M/L110M mutant of human transthyretin at pH 5.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DGD PDB entry 3DGD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 ZINC ACETATE 0.2 M, SODIUM CITRATE 0.1 M, AMMONIUM SULFATE 2,0M, CRYSTALS WERE SOAKED IN MOTHER LIQUOR SUPPLEMENTED WITH 10 % GLYCEROL BEFORE FREEZING IN LIQUID NITROGEN, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.21 44.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.495 α = 90 b = 61.615 β = 90.01 c = 47.268 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 2008-09-04 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 1.78 27.9 99.18 0.191 8.1 5.2 45854 31.6
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) 1.78 1.82 100 0.488 3 5.1 6075
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 (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 3DGD 1.78 27.9 43051 2697 99.18 0.2023 0.20508 0.20205 0.215 0.2539 0.256 RANDOM 28.895
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] 0.33 0.58 -0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.892 r_dihedral_angle_3_deg 16.962 r_dihedral_angle_4_deg 16.888 r_sphericity_free 9.772 r_dihedral_angle_1_deg 7.782 r_scangle_it 5.253 r_sphericity_bonded 4.275 r_scbond_it 3.506 r_mcangle_it 2.699 r_angle_refined_deg 1.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.892 r_dihedral_angle_3_deg 16.962 r_dihedral_angle_4_deg 16.888 r_sphericity_free 9.772 r_dihedral_angle_1_deg 7.782 r_scangle_it 5.253 r_sphericity_bonded 4.275 r_scbond_it 3.506 r_mcangle_it 2.699 r_angle_refined_deg 1.9 r_rigid_bond_restr 1.895 r_mcbond_it 1.692 r_angle_other_deg 1.016 r_mcbond_other 0.773 r_chiral_restr 0.117 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3551 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms 94
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling