☰ Navigation Tabs
Crystal structure of glutathione transferase PPUT_1760 from Pseudomonas putida, target EFI-507288, with one glutathione disulfide bound per one protein subunit
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MF6 PDB ENTRY 4MF6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 Protein in 10 mM HEPES, PH 7.5, 150 mM sodium chloride, 5% glycerol, reservoir: 20% peg1500, 20% glycerol, 5 MM GSH, cryoprotectant: NONE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K
Crystal Properties Matthews coefficient Solvent content 2.07 40.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.342 α = 90 b = 66.62 β = 90 c = 119.821 γ = 90
Symmetry Space Group P 21 21 21
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 315 MIRRORS 2013-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
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 1.3 50 99.9 0.094 9.7 7.9 116741 -5
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 1.3 1.32 100 0.66 2.5 7.7
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 4MF6 1.301 50 113148 3502 99.71 0.10146 0.10053 0.1232 0.13123 0.1474 RANDOM 21.927
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] 0.64 -0.45 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.304 r_sphericity_free 26.756 r_sphericity_bonded 16.532 r_dihedral_angle_3_deg 11.814 r_dihedral_angle_4_deg 10.924 r_rigid_bond_restr 10.918 r_scbond_other 7.506 r_scbond_it 7.505 r_scangle_other 7.453 r_long_range_B_refined 5.955
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.304 r_sphericity_free 26.756 r_sphericity_bonded 16.532 r_dihedral_angle_3_deg 11.814 r_dihedral_angle_4_deg 10.924 r_rigid_bond_restr 10.918 r_scbond_other 7.506 r_scbond_it 7.505 r_scangle_other 7.453 r_long_range_B_refined 5.955 r_long_range_B_other 5.954 r_dihedral_angle_1_deg 5.632 r_mcbond_it 3.218 r_mcbond_other 3.217 r_mcangle_it 3.135 r_mcangle_other 3.135 r_angle_refined_deg 1.431 r_angle_other_deg 0.854 r_chiral_restr 0.094 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3771 Nucleic Acid Atoms Solvent Atoms 543 Heterogen Atoms 101
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling