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Crystal structure of transthyretin variant L55P 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 400, 0.05-0.2M CaCl2, 0.1M NaHepes , pH 4.6, VAPOR DIFFUSION, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.15 42.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.632 α = 90 b = 84.78 β = 90 c = 65.415 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 210 2006-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.9340 ESRF ID14-1
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 1.85 51.3 98.1 0.062 19.8 6.3 19735 19735
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 1.85 1.95 89.7 0.434 3.5 4.2 2554
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 1.87 42.37 19703 19703 1001 96.78 0.20768 0.20692 0.2054 0.2225 0.22 RANDOM 29.867
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] -0.52 -0.31 0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.252 r_dihedral_angle_3_deg 16.475 r_dihedral_angle_4_deg 14.83 r_scangle_it 8.497 r_scbond_it 5.597 r_dihedral_angle_1_deg 5.033 r_mcangle_it 4.907 r_mcbond_it 3.165 r_angle_refined_deg 1.001 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.252 r_dihedral_angle_3_deg 16.475 r_dihedral_angle_4_deg 14.83 r_scangle_it 8.497 r_scbond_it 5.597 r_dihedral_angle_1_deg 5.033 r_mcangle_it 4.907 r_mcbond_it 3.165 r_angle_refined_deg 1.001 r_nbtor_refined 0.299 r_symmetry_vdw_refined 0.183 r_nbd_refined 0.181 r_xyhbond_nbd_refined 0.159 r_symmetry_hbond_refined 0.121 r_chiral_restr 0.067 r_bond_refined_d 0.01 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 1790 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling PHASER phasing