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Crystal structure of recombinant rat selenoprotein thioredoxin reductase 1 with reduced C-terminal tail
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H6V PDB ENTRY 1H6V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.1M HEPES, PEG 3350 15%, 12% of ethylene glycol , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.87 57.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.574 α = 90 b = 140.669 β = 94.5 c = 171.167 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 225 mm CCD mirrors 2007-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 0.978 MAX II I911-3
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 2.75 84 99.5 0.077 15.2 3.5 95938 95938 69
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.9 98.9 0.4 0.4 2.6 3.3 13890
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1H6V 2.75 29.74 91013 91013 4804 99.5 0.20799 0.20799 0.2065 0.2763 0.23602 RANDOM 63.55
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] -1.16 0.05 1.82 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.365 r_dihedral_angle_4_deg 23.25 r_dihedral_angle_3_deg 16.367 r_dihedral_angle_1_deg 6.568 r_scangle_it 2.809 r_scbond_it 1.664 r_angle_refined_deg 1.494 r_mcangle_it 1.064 r_mcbond_it 0.677 r_symmetry_hbond_refined 0.516
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.365 r_dihedral_angle_4_deg 23.25 r_dihedral_angle_3_deg 16.367 r_dihedral_angle_1_deg 6.568 r_scangle_it 2.809 r_scbond_it 1.664 r_angle_refined_deg 1.494 r_mcangle_it 1.064 r_mcbond_it 0.677 r_symmetry_hbond_refined 0.516 r_symmetry_vdw_refined 0.345 r_nbtor_refined 0.316 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.101 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 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 22574 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 510
Software Software Software Name Purpose ProDC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling