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Crystal structure of Helicobacter pylori thioredoxin reductase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A87 PDB ENTRY 2A87
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 277 2.0 M Ammonium sulfate,0.2M Ammonium Nitrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.21 61.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.4 α = 90 b = 89.4 β = 90 c = 279.9 γ = 120
Symmetry Space Group P 32 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 MARMOSAIC 225 mm CCD MIRRORS 2007-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 CLSI 08ID-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 2.43 19.98 0.068 0.068 24.31 10.5 49803 -2
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 2A87 2.43 19.98 47307 2490 100 0.181 0.178 0.1807 0.252 0.249 RANDOM 39.07
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] 0.01 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.265 r_dihedral_angle_4_deg 24.348 r_dihedral_angle_3_deg 21.942 r_dihedral_angle_1_deg 7.217 r_scangle_it 5.346 r_scbond_it 3.401 r_angle_refined_deg 2.402 r_mcangle_it 2.063 r_mcbond_it 1.246 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.265 r_dihedral_angle_4_deg 24.348 r_dihedral_angle_3_deg 21.942 r_dihedral_angle_1_deg 7.217 r_scangle_it 5.346 r_scbond_it 3.401 r_angle_refined_deg 2.402 r_mcangle_it 2.063 r_mcbond_it 1.246 r_nbtor_refined 0.317 r_nbd_refined 0.263 r_symmetry_hbond_refined 0.248 r_xyhbond_nbd_refined 0.232 r_symmetry_vdw_refined 0.223 r_chiral_restr 0.189 r_bond_refined_d 0.026 r_gen_planes_refined 0.009 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 7061 Nucleic Acid Atoms Solvent Atoms 495 Heterogen Atoms 159
Software Software Software Name Purpose XDS data scaling MrBUMP phasing REFMAC refinement XDS data reduction