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Crystal Structure of DsbA-like thioredoxin domain VF_A0457 from Vibrio fischeri
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277 0.2 M Sodium chloride, 0.1 M BIS-TRIS pH 5.5, 25 % w/v Polyehtlyene glycol 3,350, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2 38.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.807 α = 90 b = 55.737 β = 90 c = 62.521 γ = 90
Symmetry Space Group P 21 21 21
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 mirrors 2008-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9793 APS 19-ID
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 1.75 41.59 98.7 0.118 9.5 5.9 17131 17131 26.75
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 1.75 1.78 90.8 0.584 2.05 4.4 768
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.758 41.59 15926 15926 844 97.52 0.191 0.191 0.188 0.197 0.241 0.2477 RANDOM 19.103
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] -1.23 -2.29 3.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.436 r_dihedral_angle_3_deg 18.029 r_dihedral_angle_4_deg 16.519 r_dihedral_angle_1_deg 5.521 r_scangle_it 4.058 r_scbond_it 2.655 r_mcangle_it 1.652 r_angle_refined_deg 1.575 r_angle_other_deg 0.981 r_mcbond_it 0.945
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.436 r_dihedral_angle_3_deg 18.029 r_dihedral_angle_4_deg 16.519 r_dihedral_angle_1_deg 5.521 r_scangle_it 4.058 r_scbond_it 2.655 r_mcangle_it 1.652 r_angle_refined_deg 1.575 r_angle_other_deg 0.981 r_mcbond_it 0.945 r_mcbond_other 0.277 r_chiral_restr 0.091 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 1414 Nucleic Acid Atoms Solvent Atoms 170 Heterogen Atoms 1
Software Software Software Name Purpose SBC-Collect data collection HKL-3000 data collection HKL-3000 phasing MLPHARE phasing DM model building SHELXD phasing RESOLVE model building Coot model building REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling DM phasing RESOLVE phasing