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X-ray structure of Thioredoxin reductase (TrxR) from Burkholderia cenocepacia (Bc-TrxR)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TDE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 2.0 M ammonium sulphate, 0.1M Tris-HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.57 52.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.29 α = 90 b = 68.29 β = 90 c = 131.35 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 100 PIXEL DECTRIS PILATUS 6M 2024-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.00 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.32 59.14 96.8 0.074 1 22.6 18.5 15470
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.32 2.36 100 6.382 0.6 0.6 19.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.52 59.14 12026 529 95.985 0.265 0.2599 0.2599 0.3657 0.3519 70
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] 2.389 1.194 2.389 -7.749
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_2_deg 25.846 r_dihedral_angle_3_deg 19.296 r_lrange_other 14.348 r_lrange_it 14.347 r_dihedral_angle_6_deg 12.011 r_scangle_it 11.261 r_scangle_other 11.261 r_mcangle_other 10.048 r_mcangle_it 10.04 r_dihedral_angle_1_deg 7.857
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_2_deg 25.846 r_dihedral_angle_3_deg 19.296 r_lrange_other 14.348 r_lrange_it 14.347 r_dihedral_angle_6_deg 12.011 r_scangle_it 11.261 r_scangle_other 11.261 r_mcangle_other 10.048 r_mcangle_it 10.04 r_dihedral_angle_1_deg 7.857 r_scbond_it 7.352 r_scbond_other 7.34 r_mcbond_it 6.898 r_mcbond_other 6.891 r_dihedral_angle_2_deg 5.131 r_angle_refined_deg 1.654 r_angle_other_deg 0.651 r_nbd_refined 0.278 r_symmetry_nbd_refined 0.263 r_symmetry_nbd_other 0.229 r_nbd_other 0.215 r_nbtor_refined 0.188 r_xyhbond_nbd_refined 0.157 r_symmetry_xyhbond_nbd_refined 0.115 r_chiral_restr 0.102 r_symmetry_nbtor_other 0.088 r_symmetry_xyhbond_nbd_other 0.03 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_ext_dist_refined_b
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2352 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing