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Structure of homoglutathione synthetase from Glycine max in open conformation with gamma-glutamyl-cysteine bound.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other homoglutathione synthetase apoenzyme
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 2.09 41.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.88 α = 90 b = 80.95 β = 95.96 c = 89.12 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 2.1 19.8 96.5 0.108 11.4 3.6 52914 51043 29.3
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) 2.1 2.16 92.3 0.467 2.4 3.8 7984
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT homoglutathione synthetase apoenzyme 2.11 19.8 52914 50057 2635 100 0.21064 0.21064 0.20654 0.28797 0.2573 RANDOM 29.3
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] -0.02 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.958 r_dihedral_angle_4_deg 23.871 r_dihedral_angle_3_deg 21.49 r_dihedral_angle_1_deg 10.744 r_scangle_it 4.965 r_scbond_it 3.453 r_angle_refined_deg 2.548 r_mcangle_it 2.241 r_mcbond_it 1.41 r_symmetry_vdw_refined 0.333
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.958 r_dihedral_angle_4_deg 23.871 r_dihedral_angle_3_deg 21.49 r_dihedral_angle_1_deg 10.744 r_scangle_it 4.965 r_scbond_it 3.453 r_angle_refined_deg 2.548 r_mcangle_it 2.241 r_mcbond_it 1.41 r_symmetry_vdw_refined 0.333 r_nbtor_refined 0.322 r_nbd_refined 0.281 r_symmetry_hbond_refined 0.261 r_xyhbond_nbd_refined 0.224 r_chiral_restr 0.193 r_bond_refined_d 0.028 r_gen_planes_refined 0.01 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 6993 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms 48
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling