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Crystal structure of transthyretin variant T60A 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 4.6 298 15% PEG 4000, 0.05M NaAcetate, 0.1M AmmoniumAcetate , pH 4.6, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.24 45.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.586 α = 90 b = 75.907 β = 93.1 c = 107.267 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 ADSC QUANTUM 315 2008-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9729 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 2.4 107.2 99.6 0.069 14.3 4 38055 38055
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) 2.4 2.53 99.8 0.486 2.9 4.1 5558
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 1F41 2.4 107.2 36139 1900 99.54 0.20517 0.20191 0.2014 0.26743 0.2634 RANDOM 50.332
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] -0.36 -2.4 -2.37 2.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.842 r_dihedral_angle_4_deg 22.628 r_dihedral_angle_3_deg 19.527 r_dihedral_angle_1_deg 7.425 r_mcangle_it 3.794 r_scangle_it 3.206 r_mcbond_it 2.287 r_scbond_it 2.254 r_angle_refined_deg 2.215 r_symmetry_hbond_refined 0.472
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.842 r_dihedral_angle_4_deg 22.628 r_dihedral_angle_3_deg 19.527 r_dihedral_angle_1_deg 7.425 r_mcangle_it 3.794 r_scangle_it 3.206 r_mcbond_it 2.287 r_scbond_it 2.254 r_angle_refined_deg 2.215 r_symmetry_hbond_refined 0.472 r_symmetry_vdw_refined 0.35 r_nbtor_refined 0.333 r_nbd_refined 0.267 r_xyhbond_nbd_refined 0.225 r_chiral_restr 0.138 r_bond_refined_d 0.027 r_gen_planes_refined 0.01 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 7152 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling PHASER phasing