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Crystal structure of human thioredoxin C69/73S double-mutant, oxidized form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ERT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 298 1.8 M ammonium sulfate, 100 mM MES, 10 mM CoCl2, 2 mM DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.26 62.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.62 α = 90 b = 125.62 β = 90 c = 33.55 γ = 120
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 325 mm CCD RH COATED FLAT MIRROR, TOROIDAL FOCUSING MIRROR 2009-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 SSRL BL9-2
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 1.5 22.43 98.6 0.053 15.2 9.89 48316 29.9
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) 1.5 1.55 97.8 0.631 2.8 9.16
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 1ERT 1.5 22.34 48316 2445 98.6 0.185 0.184 0.1875 0.211 0.2159 RANDOM 23.87
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] 0.22 0.11 0.22 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.671 r_dihedral_angle_3_deg 14.519 r_sphericity_free 9.192 r_scangle_it 5.54 r_dihedral_angle_1_deg 5.513 r_scbond_it 3.724 r_sphericity_bonded 3.531 r_mcangle_it 2.547 r_rigid_bond_restr 1.807 r_angle_refined_deg 1.731
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.671 r_dihedral_angle_3_deg 14.519 r_sphericity_free 9.192 r_scangle_it 5.54 r_dihedral_angle_1_deg 5.513 r_scbond_it 3.724 r_sphericity_bonded 3.531 r_mcangle_it 2.547 r_rigid_bond_restr 1.807 r_angle_refined_deg 1.731 r_mcbond_it 1.664 r_angle_other_deg 0.95 r_mcbond_other 0.763 r_chiral_restr 0.104 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1642 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection CrystalClear data reduction d*TREK data scaling MOLREP phasing