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Crystal structure of human thioredoxin C69/73S double mutant, reduced form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ERT PDB ENTRY 1ERT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 298 30% PEG 4000, 200 mM ammonium acetate, 100 mM sodium citrate, 5 mM DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.92 35.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.233 α = 90 b = 46.207 β = 93.25 c = 52.33 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 MARMOSAIC 325 mm CCD RH COATED FLAT MIRROR, TOROIDAL FOCUSING MIRROR 2009-04-18 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 1.1 30 96.9 0.047 40 4.9 69644 13.3
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) 1.1 1.14 91.3 0.398 3.2 4.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1ERT 1.1 17.83 69636 3536 96.9 0.145 0.144 0.172 0.1811 RANDOM 14.96
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] 0.24 -0.03 -0.1 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.545 r_dihedral_angle_3_deg 13.645 r_scangle_it 6.128 r_dihedral_angle_1_deg 5.935 r_scbond_it 4.099 r_mcangle_it 2.757 r_mcbond_it 1.849 r_angle_refined_deg 1.698 r_rigid_bond_restr 1.632 r_angle_other_deg 0.936
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.545 r_dihedral_angle_3_deg 13.645 r_scangle_it 6.128 r_dihedral_angle_1_deg 5.935 r_scbond_it 4.099 r_mcangle_it 2.757 r_mcbond_it 1.849 r_angle_refined_deg 1.698 r_rigid_bond_restr 1.632 r_angle_other_deg 0.936 r_mcbond_other 0.626 r_chiral_restr 0.104 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 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 r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1642 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction XDS data scaling HKL-2000 data reduction