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Crystal structure of glutaredoxin domain of human thioredoxin reductase 3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2E7P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293.15 2.0M Ammonium sulphate; 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.03 39.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.13 α = 90 b = 71.13 β = 90 c = 72.291 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 MAR225 CCD Dynamically bendable mirror 2009-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.000 SLS X10SA
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 2.21 31.91 100 0.083 15.8 11.5 10544 10544 2
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 2.21 2.32 100 0.951 2.5 8.5
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 2E7P 2.21 31.91 10510 10005 505 99.69 0.19128 0.18916 0.2018 0.23271 0.2577 RANDOM 26.287
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] 0.44 0.22 0.44 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.804 r_dihedral_angle_4_deg 18.802 r_dihedral_angle_3_deg 14.233 r_scangle_it 9.887 r_scbond_it 6.587 r_dihedral_angle_1_deg 6.477 r_mcangle_it 4.215 r_mcbond_it 2.355 r_angle_refined_deg 1.33 r_angle_other_deg 0.892
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.804 r_dihedral_angle_4_deg 18.802 r_dihedral_angle_3_deg 14.233 r_scangle_it 9.887 r_scbond_it 6.587 r_dihedral_angle_1_deg 6.477 r_mcangle_it 4.215 r_mcbond_it 2.355 r_angle_refined_deg 1.33 r_angle_other_deg 0.892 r_mcbond_other 0.846 r_chiral_restr 0.082 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1640 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms 16
Software Software Software Name Purpose PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling