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Crystal structure of thioredoxin domain of thiol-disulfide oxidoreductase BVU-2223 (Target EFI-501010) from Bacteroides vulgatus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2LRN PDB ENTRY 2LRN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 2M AMMONIUM SULFATE, 0.2M SODIUM CHLORIDE, 0.1M SODIUM CACODYLATE, PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
Crystal Properties Matthews coefficient Solvent content 2.19 43.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.664 α = 90 b = 52.65 β = 90 c = 82.622 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 2012-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.76 70 99.6 0.068 13.8 5.9 15565 -5 20.918
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 1.76 1.79 100 0.44 4.7 5.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2LRN 1.76 44.4 14708 773 99.47 0.1677 0.16547 0.1775 0.21028 0.217 RANDOM 28.535
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] -0.02 -0.11 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.175 r_dihedral_angle_4_deg 14.484 r_dihedral_angle_3_deg 12.581 r_dihedral_angle_1_deg 5.208 r_angle_refined_deg 1.2 r_angle_other_deg 0.598 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.175 r_dihedral_angle_4_deg 14.484 r_dihedral_angle_3_deg 12.581 r_dihedral_angle_1_deg 5.208 r_angle_refined_deg 1.2 r_angle_other_deg 0.598 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1124 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 30
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling