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Crystal structure of E. coli Grx2: Enzyme inhibited state in complex with Zinc and glutathione sulfinic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KX4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.15 25mg/ml in 25mM Tris pH 8.0, 150 mM NaCl, 20 mM GSH, 10 mM DHA
0.01M Zinc sulfate heptahydrate, 0.1M MES monohydrate pH6.5, 25%v/v Polyethylene glycol monomethyl ether 550, Protein and reservoir mixed in 1:1, 1:2 and 2:1 ratio, set up using MRC Swissci 3 well plates with drop size 150 nl.
Crystal Properties Matthews coefficient Solvent content 2.11 41.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.095 α = 90 b = 106.758 β = 90 c = 42.13 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS PILATUS 6M-F 2017-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.984 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.6 42.35 99.3 0.191 0.208 0.082 0.995 11.7 6.3 28045
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.628 99.4 1.207 1.32 0.525 0.555 6.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4KX4 1.61 42.319 26365 1385 99.37 0.1329 0.1303 0.1305 0.1823 0.1821 RANDOM 13.839
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] -0.23 0.37 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.15 r_dihedral_angle_4_deg 16.627 r_dihedral_angle_3_deg 13.978 r_dihedral_angle_1_deg 6.359 r_rigid_bond_restr 2.958 r_angle_refined_deg 1.853 r_angle_other_deg 1.589 r_chiral_restr 0.112 r_bond_refined_d 0.016 r_gen_planes_refined 0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.15 r_dihedral_angle_4_deg 16.627 r_dihedral_angle_3_deg 13.978 r_dihedral_angle_1_deg 6.359 r_rigid_bond_restr 2.958 r_angle_refined_deg 1.853 r_angle_other_deg 1.589 r_chiral_restr 0.112 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1678 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing