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The structure of a glutathione synthetase like-effector (GSS22) from Globodera pallida in ADP-bound closed conformation.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OEV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 293.15 0.2 M tri-methylamine N-oxide, 0.1 M Tris pH 9 and 20 % w/v PEG 2000 MME with the addition of ADP (2.5 mM), MgCl2 (5 mM) and GSH (2.5 mM)
Crystal Properties Matthews coefficient Solvent content 2.86 57.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.27 α = 90 b = 121.079 β = 90 c = 128.338 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 PIXEL DECTRIS PILATUS3 6M 2015-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.98 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.57 50 100 0.147 0.154 13.7 11.1 39223
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.71 1.348 1.14
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 5OEV 2.57 50 38293 2068 99.96 0.217 0.2153 0.2161 0.2474 0.2444 RANDOM 53.378
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] 0.51 -1.09 0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.142 r_dihedral_angle_3_deg 15.619 r_dihedral_angle_4_deg 13.248 r_dihedral_angle_1_deg 6.067 r_angle_refined_deg 1.394 r_angle_other_deg 0.917 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.142 r_dihedral_angle_3_deg 15.619 r_dihedral_angle_4_deg 13.248 r_dihedral_angle_1_deg 6.067 r_angle_refined_deg 1.394 r_angle_other_deg 0.917 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6936 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2 data processing xia2 data reduction MOLREP phasing