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Crystal Structure of Mouse Transthyretin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DVQ pdb code 1dvq
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 25% PEG 2000 MME, 100 mM sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.14 42.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.511 α = 90 b = 120.511 β = 90 c = 113.186 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 IMAGE PLATE RIGAKU RAXIS IV 2007-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ DW 1.5418
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 2.05 30 100 0.076 32.5 10.7 60027 60024 38.8
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 2.05 2.12 100 0.897 2.8 5935
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 pdb code 1dvq 2.05 24.88 60088 59951 3033 99.93 0.20043 0.198 0.1975 0.24609 0.2435 RANDOM 37.317
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] 0.86 0.43 0.86 -1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.527 r_dihedral_angle_4_deg 16.528 r_dihedral_angle_3_deg 11.099 r_scangle_it 7.825 r_scbond_it 6.232 r_dihedral_angle_1_deg 5.345 r_mcangle_it 4.076 r_mcbond_it 3.441 r_mcbond_other 1.096 r_angle_refined_deg 0.988
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.527 r_dihedral_angle_4_deg 16.528 r_dihedral_angle_3_deg 11.099 r_scangle_it 7.825 r_scbond_it 6.232 r_dihedral_angle_1_deg 5.345 r_mcangle_it 4.076 r_mcbond_it 3.441 r_mcbond_other 1.096 r_angle_refined_deg 0.988 r_angle_other_deg 0.731 r_symmetry_hbond_refined 0.202 r_nbd_other 0.176 r_nbd_refined 0.171 r_nbtor_refined 0.169 r_symmetry_vdw_other 0.167 r_xyhbond_nbd_refined 0.121 r_symmetry_vdw_refined 0.106 r_nbtor_other 0.079 r_xyhbond_nbd_other 0.07 r_chiral_restr 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7133 Nucleic Acid Atoms Solvent Atoms 347 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement StructureStudio data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing