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Oxidized thioredoxin reductase from Helicobacter pylori in complex with NADP+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TDE PDB ENTRY 1TDE
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 2.35 47.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.128 α = 90 b = 99.195 β = 100.02 c = 64.436 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 1.7 63.5 98.4 0.059 0.059 5.4 3.5 66999 66999
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 1.7 1.79 90.2 0.429 0.429 1.7 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1TDE 1.7 63.5 66969 63605 3364 98.32 0.19024 0.18834 0.1955 0.22605 0.2316 RANDOM 23.304
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] 0.79 0.91 -2.18 1.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.254 r_dihedral_angle_4_deg 19.184 r_dihedral_angle_3_deg 13.722 r_dihedral_angle_1_deg 5.378 r_scangle_it 2.306 r_scbond_it 1.746 r_angle_refined_deg 1.604 r_mcangle_it 0.984 r_angle_other_deg 0.858 r_mcbond_it 0.814
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.254 r_dihedral_angle_4_deg 19.184 r_dihedral_angle_3_deg 13.722 r_dihedral_angle_1_deg 5.378 r_scangle_it 2.306 r_scbond_it 1.746 r_angle_refined_deg 1.604 r_mcangle_it 0.984 r_angle_other_deg 0.858 r_mcbond_it 0.814 r_symmetry_vdw_refined 0.23 r_mcbond_other 0.226 r_nbd_refined 0.206 r_nbd_other 0.194 r_symmetry_hbond_refined 0.193 r_symmetry_vdw_other 0.186 r_nbtor_refined 0.181 r_chiral_restr 0.165 r_xyhbond_nbd_refined 0.132 r_nbtor_other 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other 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 4688 Nucleic Acid Atoms Solvent Atoms 357 Heterogen Atoms 202
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOSFLM data reduction REFMAC phasing