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Crystal structure of a glutathione S-transferase domain-containing protein (Marinobacter aquaeolei VT8), Target EFI-507332
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ERF pdb entry 3ERF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 273 0.2M Sodium Chloride, 0.1 M Tris:HCl, 25% PEG3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 2.35 47.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.607 α = 90 b = 70.784 β = 90 c = 98.776 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 RAYONIX MX225HE 2013-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID
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 1.7 50 99.6 0.067 27.9 7.2 52271 52068
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 1.7 1.73 99.8 0.71 2.9 7.2
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 MOLECULAR REPLACEMENT THROUGHOUT pdb entry 3ERF 1.7 50 49347 2658 99.48 0.1949 0.19348 0.22059 0.2349 RANDOM 28.704
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] 1.59 -0.98 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.93 r_dihedral_angle_4_deg 14.94 r_dihedral_angle_3_deg 11.889 r_long_range_B_refined 6.926 r_long_range_B_other 6.836 r_dihedral_angle_1_deg 5.652 r_scangle_other 5.639 r_mcangle_it 3.979 r_mcangle_other 3.979 r_scbond_it 3.952
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.93 r_dihedral_angle_4_deg 14.94 r_dihedral_angle_3_deg 11.889 r_long_range_B_refined 6.926 r_long_range_B_other 6.836 r_dihedral_angle_1_deg 5.652 r_scangle_other 5.639 r_mcangle_it 3.979 r_mcangle_other 3.979 r_scbond_it 3.952 r_scbond_other 3.951 r_mcbond_it 2.897 r_mcbond_other 2.894 r_angle_refined_deg 1.406 r_angle_other_deg 0.894 r_chiral_restr 0.097 r_bond_refined_d 0.013 r_gen_planes_refined 0.013 r_gen_planes_other 0.006 r_bond_other_d 0.004 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3190 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling