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Crystal structure of transthyretin variant L58H 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 32% PEG 2000, 0.1M NaAc, 0.2M Am2SO4 , pH 4.6, VAPOR DIFFUSION, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.19 43.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.846 α = 90 b = 85.694 β = 90 c = 64.478 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 2006-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.979 ESRF ID23-1
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 1.8 64.42 99.4 0.103 16.4 6.7 23088 23088
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 1.8 1.9 100 0.342 5.3 7 3343
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 1.8 64.42 23052 23052 1184 99.28 0.20478 0.2041 0.2019 0.21742 0.2163 RANDOM 26.831
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] -0.12 0.07 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.16 r_dihedral_angle_4_deg 19.148 r_dihedral_angle_3_deg 17.571 r_scangle_it 9.957 r_scbond_it 8.003 r_dihedral_angle_1_deg 5.69 r_mcangle_it 4.691 r_mcbond_it 3.179 r_angle_refined_deg 1.464 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.16 r_dihedral_angle_4_deg 19.148 r_dihedral_angle_3_deg 17.571 r_scangle_it 9.957 r_scbond_it 8.003 r_dihedral_angle_1_deg 5.69 r_mcangle_it 4.691 r_mcbond_it 3.179 r_angle_refined_deg 1.464 r_nbtor_refined 0.316 r_symmetry_vdw_refined 0.243 r_nbd_refined 0.238 r_xyhbond_nbd_refined 0.19 r_chiral_restr 0.097 r_symmetry_hbond_refined 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 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 1796 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling PHASES phasing