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Apoenzyme structure of homoglutathione synthetase from Glycine max in open conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HGS human glutathione synthetase, 2HGS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 20% PEG3000, 0.1 M 3-(N-morpholino)-2-hydroxypropanesulfonic acid (MOPSO), pH
7, 0.2 M MgSO4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.1 41.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.957 α = 90 b = 80.549 β = 96.94 c = 89.995 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 2007-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.979 SSRL BL9-1
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 28.4 94.8 0.069 13.7 2.2 62342 59099 26
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) 2 2.05 86.8 0.379 3.4 2.1 8652
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 human glutathione synthetase, 2HGS 2 28.38 59099 57570 3031 100 0.20151 0.20151 0.19795 0.2025 0.26859 0.27 RANDOM 25.989
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] -0.03 -0.01 0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.276 r_dihedral_angle_4_deg 21.708 r_dihedral_angle_3_deg 18.714 r_dihedral_angle_1_deg 8.112 r_scangle_it 4.34 r_scbond_it 2.93 r_angle_refined_deg 2.032 r_mcangle_it 1.964 r_mcbond_it 1.257 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.276 r_dihedral_angle_4_deg 21.708 r_dihedral_angle_3_deg 18.714 r_dihedral_angle_1_deg 8.112 r_scangle_it 4.34 r_scbond_it 2.93 r_angle_refined_deg 2.032 r_mcangle_it 1.964 r_mcbond_it 1.257 r_nbtor_refined 0.312 r_nbd_refined 0.258 r_symmetry_hbond_refined 0.253 r_symmetry_vdw_refined 0.242 r_xyhbond_nbd_refined 0.213 r_chiral_restr 0.179 r_bond_refined_d 0.021 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7108 Nucleic Acid Atoms Solvent Atoms 469 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling