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Crystal structure of a periplasmic thioredoxin-like protein from Salmonella enterica serovar Typhimurium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GYK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.2 298 18-27% (w/v) PEG 4000, 0.1M Tris buffer pH 8.2 , VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.32 46.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.107 α = 90 b = 90.998 β = 102.23 c = 83.309 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 IMAGE PLATE RIGAKU RAXIS IV++ 2011-08-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.541
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 1.98 48.69 99.97 0.065 13 7.45 106172 106150 3 3 35.41
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 1.98 2.05 100 0.479 2.4 7.29 10617
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 3GYK 2.04 48.689 49333 49220 2506 99.77 0.2018 0.2018 0.1992 0.1909 0.2526 0.242 RANDOM 44.5163
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] -9.5202 -1.0006 -2.7511 12.2714
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.653 f_angle_d 1.003 f_chiral_restr 0.07 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5462 Nucleic Acid Atoms Solvent Atoms 411 Heterogen Atoms
Software Software Software Name Purpose CrystalClear data collection BALBES phasing PHENIX refinement CrystalClear data reduction CrystalClear data scaling