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The structure of a glutathione synthetase like-effector (GSS22) from Globodera pallida in apoform.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KAL
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
Crystal Properties Matthews coefficient Solvent content 2.3 46.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.258 α = 90 b = 122.393 β = 97.61 c = 132.769 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 PIXEL DECTRIS PILATUS3 6M 2015-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.917 Diamond I04-1
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 2.18 50 100 0.07 0.076 17 7.2 99955
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 2.2 2.24 0.839 0.903
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3KAL 2.18 50 97815 5118 99.96 0.2163 0.2152 0.237 0.2271 RANDOM 46.949
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] -2.21 -0.09 1.05 1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.884 r_dihedral_angle_4_deg 14.691 r_dihedral_angle_3_deg 13.548 r_dihedral_angle_1_deg 5.743 r_angle_refined_deg 1.263 r_angle_other_deg 0.908 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.884 r_dihedral_angle_4_deg 14.691 r_dihedral_angle_3_deg 13.548 r_dihedral_angle_1_deg 5.743 r_angle_refined_deg 1.263 r_angle_other_deg 0.908 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13470 Nucleic Acid Atoms Solvent Atoms 365 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction xia2 data processing MOLREP phasing