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Crystal structure of transthyretin variant V30M 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 43.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.782 α = 90 b = 86.064 β = 90 c = 64.231 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 2006-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9859 ESRF ID14-4
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 2.2 86.07 97.6 0.094 12 3.3 12491 12491
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 2.2 2.32 94.9 0.326 5.5 3 1716
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 2.3 51.5 1 12491 10880 526 97.82 0.2151 0.21313 0.2144 0.25338 0.2154 RANDOM 31.92
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] 0.94 -0.85 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.866 r_dihedral_angle_4_deg 24.739 r_dihedral_angle_3_deg 20.445 r_scangle_it 7.112 r_dihedral_angle_1_deg 6.031 r_scbond_it 5.4 r_mcangle_it 5.277 r_mcbond_it 3.802 r_angle_refined_deg 1.792 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.866 r_dihedral_angle_4_deg 24.739 r_dihedral_angle_3_deg 20.445 r_scangle_it 7.112 r_dihedral_angle_1_deg 6.031 r_scbond_it 5.4 r_mcangle_it 5.277 r_mcbond_it 3.802 r_angle_refined_deg 1.792 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.231 r_nbd_refined 0.223 r_xyhbond_nbd_refined 0.174 r_chiral_restr 0.135 r_symmetry_hbond_refined 0.114 r_bond_refined_d 0.025 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 1787 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling PHASER phasing