☰ Navigation Tabs
Tetrameric form of rat selenoprotein thioredoxin reductase 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EAN PDB ENTRY 3EAN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 45 % MPD and 100 mM Tris-Cl buffer , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.14 70.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 162.99 α = 90 b = 162.99 β = 90 c = 236.44 γ = 120
Symmetry Space Group P 31 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 2009-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2
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 2.4 70 97.3 0.094 8.5 3.9 137497 137497
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 2.4 2.53 90 0.67 1.7 3.6
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 (All) 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 3EAN 2.4 60.67 134215 134215 7095 99.59 0.1615 0.1615 0.16015 0.1699 0.18708 0.1921 RANDOM 61.197
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] 0.54 0.54 0.54 -1.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.047 r_dihedral_angle_4_deg 19.246 r_dihedral_angle_3_deg 13.721 r_dihedral_angle_1_deg 5.917 r_angle_refined_deg 1.816 r_angle_other_deg 1.202 r_chiral_restr 0.104 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.047 r_dihedral_angle_4_deg 19.246 r_dihedral_angle_3_deg 13.721 r_dihedral_angle_1_deg 5.917 r_angle_refined_deg 1.816 r_angle_other_deg 1.202 r_chiral_restr 0.104 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 0.008 r_gen_planes_other 0.007 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14940 Nucleic Acid Atoms Solvent Atoms 524 Heterogen Atoms 296
Software Software Software Name Purpose MxCuBE data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling