☰ Navigation Tabs
Crystal structure of human thioesterase 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FLB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 298 Rod-shaped crystals of TE2 (10 mg/ml with 10 mM fresh DTT) were grown using the vapor diffusion method at 25 C, using a 1:1 drop to well ratio. The well solutions contained 1.64 M NaH2PO4, 0.42 M K2HPO4 and 50 mM HEPES. Crystals were cryoprotected by transfer to paratone.
Crystal Properties Matthews coefficient Solvent content 3.02 62.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.07 α = 90 b = 96.07 β = 90 c = 159.96 γ = 90
Symmetry Space Group I 4 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV 2013-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
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 2.8 24.817 99.9 0.087 12.8 11.7 9601 9601 66.47
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 2.8 2.9 100 0.487 2.9 11.82 950
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 FREE R-VALUE 3FLB 2.8 24.817 1.34 9353 473 97.55 0.2969 0.2944 0.3127 0.3449 0.3509 94.6564
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 13.216 f_angle_d 0.725 f_chiral_restr 0.028 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1702 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement d*TREK data reduction PDB_EXTRACT data extraction d*TREK data scaling PHENIX phasing