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Glutathione transferase from Glycine max
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OYJ PDB ENTRY 1OYJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 PEG
Crystal Properties Matthews coefficient Solvent content 2.4 49.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.375 α = 90 b = 91.375 β = 90 c = 111.83 γ = 90
Symmetry Space Group P 41 21 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 MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 EMBL/DESY, HAMBURG X11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.75 70.71 98.9 0.05 42 48045 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 100 0.52 4.1
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 PDB ENTRY 1OYJ 1.75 70.71 45117 2400 98.9 0.197 0.194 0.1946 0.243 0.2429 RANDOM 26.71
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] 0.22 0.22 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.227 r_dihedral_angle_4_deg 17.161 r_dihedral_angle_3_deg 15.984 r_dihedral_angle_1_deg 10.064 r_scangle_it 3.721 r_scbond_it 2.411 r_angle_refined_deg 1.634 r_mcangle_it 1.483 r_mcbond_it 0.942 r_xyhbond_nbd_refined 0.454
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.227 r_dihedral_angle_4_deg 17.161 r_dihedral_angle_3_deg 15.984 r_dihedral_angle_1_deg 10.064 r_scangle_it 3.721 r_scbond_it 2.411 r_angle_refined_deg 1.634 r_mcangle_it 1.483 r_mcbond_it 0.942 r_xyhbond_nbd_refined 0.454 r_nbtor_refined 0.313 r_symmetry_hbond_refined 0.274 r_symmetry_vdw_refined 0.253 r_nbd_refined 0.219 r_chiral_restr 0.128 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3622 Nucleic Acid Atoms Solvent Atoms 430 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement HKL data reduction SCALEPACK data scaling PHASER phasing