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Helicobacter pylori thioredoxin reductase reduced by sodium dithionite in complex with NADP+
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 22% PEG 3350, 0.1M MIB pH 6.0, 8mM pentaethylene glycol monooctyl ether, EVAPORATION, temperature 293K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.4 48.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.451 α = 90 b = 99.455 β = 97.94 c = 64.765 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 100 CCD ADSC QUANTUM 315 2006-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9393 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.45 64.15 94.5 0.057 0.057 5.2 3.5 105645 105645 14.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.53 69.7 0.19 0.19 3.6 2.8 11370
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 FOURIER SYNTHESIS THROUGHOUT 1.45 64.15 105611 105611 5277 94.48 0.168 0.168 0.167 0.1671 0.193 0.1919 RANDOM 12.621
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] 0.06 0.07 0.17 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.878 r_dihedral_angle_4_deg 18.87 r_dihedral_angle_3_deg 11.721 r_dihedral_angle_1_deg 5.064 r_sphericity_free 4.177 r_scangle_it 2.79 r_scbond_it 2.169 r_sphericity_bonded 1.94 r_angle_refined_deg 1.495 r_mcangle_it 1.433
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.878 r_dihedral_angle_4_deg 18.87 r_dihedral_angle_3_deg 11.721 r_dihedral_angle_1_deg 5.064 r_sphericity_free 4.177 r_scangle_it 2.79 r_scbond_it 2.169 r_sphericity_bonded 1.94 r_angle_refined_deg 1.495 r_mcangle_it 1.433 r_mcbond_it 1.224 r_rigid_bond_restr 1.155 r_angle_other_deg 0.828 r_mcbond_other 0.335 r_nbd_refined 0.205 r_chiral_restr 0.204 r_nbd_other 0.191 r_nbtor_refined 0.181 r_symmetry_vdw_other 0.143 r_symmetry_vdw_refined 0.12 r_xyhbond_nbd_refined 0.118 r_symmetry_hbond_refined 0.09 r_nbtor_other 0.089 r_xyhbond_nbd_other 0.017 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4708 Nucleic Acid Atoms Solvent Atoms 530 Heterogen Atoms 202
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOSFLM data reduction