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Crystal structure of the Xi glutathione transferase ECM4 from Saccharomyces cerevisiae in complex with glutathione
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PPU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 277 20% (w/v) PEG 2000 MME, 0.1 M Tris pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.06 40.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.44 α = 90 b = 82.44 β = 95.31 c = 80.58 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 ADSC QUANTUM 315r 2015-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.979767 ESRF BM30A
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 1.68 47.59 95 0.055 0.99 17.9 3.8 78066
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.68 1.72 74.3 0.76 1.9 3.7
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 3PPU 1.68 47.582 1.36 78008 3899 94.99 0.161 0.1589 0.1617 0.2003 0.2015
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 13.803 f_angle_d 1.456 f_chiral_restr 0.085 f_bond_d 0.019 f_plane_restr 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5733 Nucleic Acid Atoms Solvent Atoms 638 Heterogen Atoms 40
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling MOLREP phasing