☰ Navigation Tabs
Structure of the Thioredoxin-like Domain of Yeast Glutaredoxin 3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ERT PDB Entry 1ERT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 290 0.1M MOPS, 20mM 2-ME, 68% ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.29 46.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.906 α = 90 b = 48.611 β = 116.76 c = 55.294 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 300 mm CCD 2007-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
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 1.5 50 95.9 0.062 18.7 3.5 35163 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) 1.5 1.55 69.1 0.347 1.9 2534
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 THROUGHOUT PDB Entry 1ERT 1.5 49.39 35147 1752 95.74 0.225 0.223 0.2244 0.249 0.2483 RANDOM 18.605
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] -0.17 -0.1 -0.08 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.35 r_dihedral_angle_3_deg 12.303 r_dihedral_angle_1_deg 5.077 r_scangle_it 4.002 r_scbond_it 2.735 r_mcangle_it 1.847 r_angle_refined_deg 1.302 r_mcbond_it 1.107 r_nbtor_refined 0.312 r_nbd_refined 0.208
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.35 r_dihedral_angle_3_deg 12.303 r_dihedral_angle_1_deg 5.077 r_scangle_it 4.002 r_scbond_it 2.735 r_mcangle_it 1.847 r_angle_refined_deg 1.302 r_mcbond_it 1.107 r_nbtor_refined 0.312 r_nbd_refined 0.208 r_symmetry_vdw_refined 0.183 r_xyhbond_nbd_refined 0.15 r_symmetry_hbond_refined 0.104 r_chiral_restr 0.078 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1721 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 10
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction SERGUI data collection HKL-2000 data reduction AMoRE phasing