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Crystal structure of human thioredoxin reductase 1
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, SITTING DROP 150 UL SITTING DROPS, 20% PEG3350, 0.1 M TRIS PH 7, ADDITIVE: NSDB-221
Crystal Properties Matthews coefficient Solvent content 3.1 61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.756 α = 90 b = 149.651 β = 91.96 c = 146.789 γ = 90
Symmetry Space Group P 1 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 ADSC CCD MIRRORS 2006-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 ALS 8.2.1
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 2.7 47 95 0.11 7 3.25 100946 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 2.7 2.8 93 0.46 2 2.9
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 1H6V 2.7 149.07 95921 5025 95 0.205 0.203 0.248 0.258 RANDOM 36.24
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] -1.11 -0.35 1.56 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.326 r_dihedral_angle_4_deg 20.16 r_dihedral_angle_3_deg 16.772 r_dihedral_angle_1_deg 5.4 r_scangle_it 1.942 r_angle_refined_deg 1.252 r_scbond_it 1.148 r_angle_other_deg 0.916 r_mcangle_it 0.785 r_mcbond_it 0.464
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.326 r_dihedral_angle_4_deg 20.16 r_dihedral_angle_3_deg 16.772 r_dihedral_angle_1_deg 5.4 r_scangle_it 1.942 r_angle_refined_deg 1.252 r_scbond_it 1.148 r_angle_other_deg 0.916 r_mcangle_it 0.785 r_mcbond_it 0.464 r_symmetry_vdw_other 0.229 r_nbd_refined 0.217 r_nbd_other 0.187 r_nbtor_refined 0.183 r_symmetry_hbond_refined 0.137 r_symmetry_vdw_refined 0.133 r_xyhbond_nbd_refined 0.124 r_nbtor_other 0.085 r_chiral_restr 0.078 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21968 Nucleic Acid Atoms Solvent Atoms 228 Heterogen Atoms 272
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing