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Crystal structure of transthyretin variant Y114H at acidic pH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F41
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.6 295 Na Citrate 0.1 M, Ammonium sulfate 2M , pH 4.6, VAPOR DIFFUSION, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.07 40.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.341 α = 90 b = 85.784 β = 90 c = 62.652 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 ADSC QUANTUM 315 2007-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9762 ESRF ID29
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 2.35 85.75 99.8 0.069 17.1 6.6 9985 9985
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 2.35 2.48 100 0.394 3.8 6.9 1409
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 (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 1F41 2.35 62.7 9666 9666 460 99.78 0.21875 0.21737 0.2259 0.24701 0.2581 RANDOM 46.796
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] 1.03 -0.64 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.812 r_dihedral_angle_4_deg 29.181 r_dihedral_angle_3_deg 21.828 r_scangle_it 13.218 r_scbond_it 9.558 r_mcangle_it 8.632 r_mcbond_it 5.957 r_dihedral_angle_1_deg 4.384 r_angle_refined_deg 1.552 r_nbtor_refined 0.335
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.812 r_dihedral_angle_4_deg 29.181 r_dihedral_angle_3_deg 21.828 r_scangle_it 13.218 r_scbond_it 9.558 r_mcangle_it 8.632 r_mcbond_it 5.957 r_dihedral_angle_1_deg 4.384 r_angle_refined_deg 1.552 r_nbtor_refined 0.335 r_nbd_refined 0.262 r_symmetry_vdw_refined 0.26 r_symmetry_hbond_refined 0.26 r_xyhbond_nbd_refined 0.241 r_chiral_restr 0.043 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 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 1788 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling