☰ Navigation Tabs
Crystal structure of ancestral thioredoxin, relative to the last common ancestor of the Cyanobacterial, Deinococcus and Thermus groups, LPBCA-L89K mutant.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YJ7 PDB ENTRY 2YJ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4 COUNTERDIFFUSION METHOD: 0.1M NA ACETATE PH 4.0, 20% PEG 400, 15% PEG 4000 & 10% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.3 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.172 α = 90 b = 38.882 β = 90 c = 61.04 γ = 90
Symmetry Space Group P 21 21 21
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 QUANTUM 315 2013-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A ESRF BM30A
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 2.35 32.79 100 0.17 11.14 6.8 3761 2 29.79
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 2.35 2.43 100 1.07 2.06 7
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 2YJ7 2.35 32.794 1.34 3756 167 99.81 0.2012 0.1992 0.2046 0.2437 0.242 36.1
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.493 f_angle_d 0.737 f_chiral_restr 0.028 f_plane_restr 0.005 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 835 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHASER phasing