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Crystal structure of glutathione transferase (TARGET EFI-501774) from methylococcus capsulatus str. bath
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DSA PDB ENTRY 2DSA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 0.2M SODIUM CHLORIDE, 0.1M TRIS-HCL, 30% PEG3000, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties Matthews coefficient Solvent content 3.5 64.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.246 α = 90 b = 129.246 β = 90 c = 129.246 γ = 90
Symmetry Space Group P 43 3 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 ADSC QUANTUM 315 MIRRORS 2011-10-07 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 2.7 50 99.6 0.084 8.9 11.9 10645 -5 114.943
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.75 100 0.8 11.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MR THROUGHOUT PDB ENTRY 2DSA 2.8 43.08 9260 281 99.51 0.19464 0.19272 0.25921 0.2478 RANDOM 102.557
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.623 r_dihedral_angle_3_deg 17.629 r_dihedral_angle_4_deg 16.097 r_scangle_it 11.787 r_scbond_it 7.555 r_mcangle_it 5.401 r_dihedral_angle_1_deg 4.789 r_mcbond_it 2.856 r_angle_refined_deg 1.05 r_chiral_restr 0.058
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.623 r_dihedral_angle_3_deg 17.629 r_dihedral_angle_4_deg 16.097 r_scangle_it 11.787 r_scbond_it 7.555 r_mcangle_it 5.401 r_dihedral_angle_1_deg 4.789 r_mcbond_it 2.856 r_angle_refined_deg 1.05 r_chiral_restr 0.058 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1607 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 6
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling