☰ Navigation Tabs
Crystal structure of a reconstructed ancestor of Triosephosphate isomerase from eukaryotes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I9E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 0.1M HEPS pH 7.5, 20% PEG 8000.
Protein concentration 6 mg/mL in 10 mM Triethanolamine pH 7.6, 1 mM EDTA, 1 mM DTT, 50 mM NaCl, 10 mM PGH
Crystal Properties Matthews coefficient Solvent content 2.32 46.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.02 α = 91.28 b = 48.772 β = 100.14 c = 71.205 γ = 118.65
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 103 IMAGE PLATE RIGAKU RAXIS IV++ Mirror 2016-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.9 42.472 95 0.071 0.997 12.3 3.9 37060 22.52
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 1.9 1.968 91.4 0.454 3 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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 THROUGHOUT 2I9E 1.9 38.423 1.94 37057 1871 94.73 0.1646 0.1625 0.1632 0.2017 0.2004
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 8.23 f_angle_d 0.96 f_chiral_restr 0.06 f_bond_d 0.01 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3817 Nucleic Acid Atoms Solvent Atoms 427 Heterogen Atoms 20
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHASER phasing