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Crystal structure of transthyretin variant V20S
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 7.5 295 0.066M CaCl2, 19% (w/v) PEG 400, 0.13M sodium Hepes , pH 7.5, VAPOR DIFFUSION, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.1 41.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.999 α = 90 b = 83.812 β = 90 c = 65.58 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 2005-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.92 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 1.59 65.51 99.1 0.051 17.3 3.2 30276 30276
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) 1.59 1.63 92.9 0.423 2.1 2 2071
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 (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 1F41 1.59 22 32076 30276 1618 99.14 0.2102 0.20966 0.20862 0.2077 0.22911 0.2291 RANDOM 17.842
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] -0.59 0.24 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.349 r_dihedral_angle_4_deg 15.53 r_dihedral_angle_3_deg 11.472 r_dihedral_angle_1_deg 7.661 r_scangle_it 2.968 r_mcangle_it 2.521 r_scbond_it 2.012 r_mcbond_it 1.965 r_angle_refined_deg 1.286 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.349 r_dihedral_angle_4_deg 15.53 r_dihedral_angle_3_deg 11.472 r_dihedral_angle_1_deg 7.661 r_scangle_it 2.968 r_mcangle_it 2.521 r_scbond_it 2.012 r_mcbond_it 1.965 r_angle_refined_deg 1.286 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.205 r_nbd_refined 0.201 r_symmetry_hbond_refined 0.123 r_xyhbond_nbd_refined 0.104 r_chiral_restr 0.098 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 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 140 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling AMoRE phasing