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Crystal structure of Drosophila melanogaster Noppera-bo, glutathione S-transferase epsilon 14 (DmGSTE14), in TDP013-bound form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6KEM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 293 34% (v/v) PPG 400, 80mM Bis-Tris, pH 6.4
Crystal Properties Matthews coefficient Solvent content 2.16 43.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.696 α = 90 b = 75.069 β = 90 c = 108.253 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 315r 2015-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.00000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.7 31.6218017005 99.46 0.0337 0.365 1 36.69 6.9 53049 2 17.63
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.761 95.77 0.1828 0.973 7.94 4.9
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6KEM 1.70000976227 31.6218017005 1.35268350705 53045 2676 99.4711872035 0.169107160218 0.167536896626 0.199069133595 0.1991 21.43528988
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 14.0411169073 f_angle_d 1.27972862664 f_chiral_restr 0.0444770419302 f_bond_d 0.00746794033198 f_plane_restr 0.00640122102376
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3515 Nucleic Acid Atoms Solvent Atoms 438 Heterogen Atoms 81
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling MOLREP phasing