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Crystal structure of a glutathione S-transferase from Rhodospirillum rubrum F11, Target EFI-507460
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MDC pdb entry 4MDC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 273 0.17 M Sodium Acetate, 0.085 M Tris:HCl, 25.5% (w/v) PEG 4000, 15% (v/v) Glycerol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 2.24 45.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.084 α = 109.85 b = 48.965 β = 106.96 c = 56.559 γ = 95.2
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 RAYONIX MX225HE 2013-08-13 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 1.6 50 96.7 0.074 18.5 3.9 58987 57020
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 1.6 1.63 90.3 0.404 2.9 3.5
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 4MDC 1.6 49.95 54113 2907 96.52 0.17713 0.17598 0.1885 0.1979 0.2054 RANDOM 19.207
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] 0.56 0.42 0.32 0.41 -0.62 -0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.356 r_dihedral_angle_4_deg 19.891 r_dihedral_angle_3_deg 12.873 r_dihedral_angle_1_deg 5.501 r_long_range_B_refined 4.48 r_long_range_B_other 4.447 r_scangle_other 3.19 r_mcangle_it 2.315 r_mcangle_other 2.314 r_scbond_it 2.053
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.356 r_dihedral_angle_4_deg 19.891 r_dihedral_angle_3_deg 12.873 r_dihedral_angle_1_deg 5.501 r_long_range_B_refined 4.48 r_long_range_B_other 4.447 r_scangle_other 3.19 r_mcangle_it 2.315 r_mcangle_other 2.314 r_scbond_it 2.053 r_scbond_other 2.051 r_angle_refined_deg 1.551 r_mcbond_it 1.523 r_mcbond_other 1.522 r_angle_other_deg 0.878 r_chiral_restr 0.089 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.002 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 3554 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling