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Crystal structure of the wild type Thioredoxin glutatione reductase from Schistosoma mansoni in complex with auranofin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V6O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 Hepes pH 7.0, 20% PEG3350, 0.1M KI, 5mM GSH, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.2 61.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.515 α = 90 b = 102.166 β = 114.16 c = 60.572 γ = 90
Symmetry Space Group C 1 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 CCD MAR CCD 165 mm 2008-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.98 BESSY 14.1
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 2.55 40 99.7 0.12 14.7 5.2 26954 47.3
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 2.55 2.59 0.48 2.4 5.2 1329
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 2v6o 2.55 40 25362 1346 99.64 0.23145 0.23014 0.2312 0.2563 0.2598 RANDOM 35.425
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] 2.92 0.68 -2.64 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.147 r_dihedral_angle_3_deg 12.677 r_dihedral_angle_4_deg 10.384 r_dihedral_angle_1_deg 4.657 r_angle_refined_deg 0.913 r_scangle_it 0.679 r_mcangle_it 0.433 r_scbond_it 0.406 r_nbtor_refined 0.29 r_mcbond_it 0.234
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.147 r_dihedral_angle_3_deg 12.677 r_dihedral_angle_4_deg 10.384 r_dihedral_angle_1_deg 4.657 r_angle_refined_deg 0.913 r_scangle_it 0.679 r_mcangle_it 0.433 r_scbond_it 0.406 r_nbtor_refined 0.29 r_mcbond_it 0.234 r_nbd_refined 0.164 r_symmetry_vdw_refined 0.141 r_xyhbond_nbd_refined 0.11 r_symmetry_hbond_refined 0.097 r_chiral_restr 0.057 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 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 4503 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 103
Software Software Software Name Purpose HKL-2000 data collection PHASES phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling