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Crystal structure of plant glutamate cysteine ligase in complex with Mg2+ and L-glutamate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GWC 2GWC monomer
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 18% PEG 3350, 0.2 M magnesium acetate tetrahydrate, 0.1 M tricine, 0.05 M L-glutamate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.2 44.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.81 α = 90 b = 54.81 β = 90 c = 518.04 γ = 120
Symmetry Space Group P 61 2 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 CCD Large Area Detector 2004-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.9782 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.09 47.46 94.8 0.062 27.2 11 27931 27931 -3 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.09 2.22 70.5 0.13 5.7 2.1 3283
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2GWC monomer 2.09 47.46 -3 27818 26427 1391 100 0.178 0.178 0.17532 0.1867 0.2267 0.2295 RANDOM 20.333
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] 0.12 0.06 0.12 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.32 r_dihedral_angle_4_deg 17.123 r_dihedral_angle_3_deg 13.95 r_dihedral_angle_1_deg 6.319 r_scangle_it 2.323 r_scbond_it 1.604 r_angle_refined_deg 1.314 r_mcangle_it 0.821 r_angle_other_deg 0.812 r_mcbond_it 0.722
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.32 r_dihedral_angle_4_deg 17.123 r_dihedral_angle_3_deg 13.95 r_dihedral_angle_1_deg 6.319 r_scangle_it 2.323 r_scbond_it 1.604 r_angle_refined_deg 1.314 r_mcangle_it 0.821 r_angle_other_deg 0.812 r_mcbond_it 0.722 r_nbd_refined 0.21 r_symmetry_vdw_other 0.209 r_nbd_other 0.185 r_symmetry_vdw_refined 0.183 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.142 r_mcbond_other 0.136 r_nbtor_other 0.083 r_symmetry_hbond_refined 0.075 r_chiral_restr 0.073 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3495 Nucleic Acid Atoms Solvent Atoms 245 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement XDS data scaling PHASER phasing