☰ Navigation Tabs
Crystal Structure of Thioredoxin Reductase from Drosophila melanogaster
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H6V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 200 mM Succinate, 22% PEG 6000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.8 56.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.487 α = 90 b = 151.487 β = 90 c = 134.259 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 104 IMAGE PLATE MAR scanner 345 mm plate Xenocs FOX-2D Multilayer Mirrors 2006-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 15 98.7 0.059 13.2 7.85 22987
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 90.3 0.422 2.78 2075
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1H6V 2.4 15 21869 2201 93.84 0.203 0.198 0.1955 0.247 0.2452 RANDOM 49.14
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] 1.7 0.85 1.7 -2.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.685 r_dihedral_angle_4_deg 19.865 r_dihedral_angle_3_deg 18.707 r_dihedral_angle_1_deg 6.15 r_scangle_it 1.836 r_angle_refined_deg 1.359 r_scbond_it 1.12 r_mcangle_it 0.761 r_mcbond_it 0.425 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.685 r_dihedral_angle_4_deg 19.865 r_dihedral_angle_3_deg 18.707 r_dihedral_angle_1_deg 6.15 r_scangle_it 1.836 r_angle_refined_deg 1.359 r_scbond_it 1.12 r_mcangle_it 0.761 r_mcbond_it 0.425 r_nbtor_refined 0.304 r_nbd_refined 0.214 r_symmetry_vdw_refined 0.2 r_symmetry_hbond_refined 0.197 r_xyhbond_nbd_refined 0.13 r_chiral_restr 0.095 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3670 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection DENZO data reduction SCALEPACK data scaling CNS phasing