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Transthyretin-like protein from Salmonella dublin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SN0 PDB ENTRY 1SN0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 295 20% PEG 3350, 0.2M magnesium chloride, 0.1M sodium cacodylate, pH 6.0, EVAPORATION, RECRYSTALLIZATION, temperature 295K, pH 6.00
Crystal Properties Matthews coefficient Solvent content 2.93 58.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.705 α = 90 b = 94.705 β = 90 c = 57.381 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV MIRRORS 2005-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ELLIOTT GX-13
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.497 82.017 99.5 0.111 0.111 6.5 5 10308
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.49 2.63 0.457 0.457 1.6 2.9
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 ENTRY 1SN0 2.5 81.92 10306 10306 496 99.8 0.228 0.226 0.2369 0.261 0.2375 RANDOM 24.36
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] -0.69 -0.35 -0.69 1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.307 r_dihedral_angle_3_deg 16.602 r_dihedral_angle_4_deg 9.216 r_dihedral_angle_1_deg 6.014 r_scangle_it 2.084 r_scbond_it 1.424 r_angle_refined_deg 1.193 r_mcangle_it 0.969 r_mcbond_it 0.529 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.307 r_dihedral_angle_3_deg 16.602 r_dihedral_angle_4_deg 9.216 r_dihedral_angle_1_deg 6.014 r_scangle_it 2.084 r_scbond_it 1.424 r_angle_refined_deg 1.193 r_mcangle_it 0.969 r_mcbond_it 0.529 r_nbtor_refined 0.302 r_nbd_refined 0.162 r_symmetry_vdw_refined 0.159 r_xyhbond_nbd_refined 0.123 r_chiral_restr 0.117 r_symmetry_hbond_refined 0.098 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 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 1732 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 10
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling