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1.55 Angstrom Resolution Crystal Structure of Glutathione Reductase from Yersinia pestis in Complex with FAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GES
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.3 295 Protein: 10.0 mg/ml, 0.01M Tris HCl (pH 8.3);
Screen: Classics II (B6), 0.49M Sodium phosphate, 0.91M Potassium phosphate;
Cryo: Screen : 50% Sucrose (1:1)
Crystal Properties Matthews coefficient Solvent content 2.73 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.844 α = 90 b = 125.844 β = 90 c = 124.557 γ = 120
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 MARMOSAIC 300 mm CCD C(111) 2017-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rpim I (All) 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 1.55 30 100 0.06 0.06 0.025 25.3 6.3 161196 -3 19.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.58 100 0.721 0.721 0.319 0.729 2.3 6
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 1GES 1.55 29.94 153253 7895 99.82 0.14567 0.14471 0.16456 0.1681 RANDOM 20.379
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] 0.07 0.03 0.07 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.866 r_dihedral_angle_3_deg 9.136 r_dihedral_angle_4_deg 8.626 r_long_range_B_refined 5.852 r_long_range_B_other 5.356 r_dihedral_angle_1_deg 3.749 r_scangle_other 2.893 r_scbond_it 1.866 r_scbond_other 1.866 r_angle_refined_deg 1.508
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.866 r_dihedral_angle_3_deg 9.136 r_dihedral_angle_4_deg 8.626 r_long_range_B_refined 5.852 r_long_range_B_other 5.356 r_dihedral_angle_1_deg 3.749 r_scangle_other 2.893 r_scbond_it 1.866 r_scbond_other 1.866 r_angle_refined_deg 1.508 r_mcangle_it 1.353 r_mcangle_other 1.353 r_angle_other_deg 0.873 r_mcbond_it 0.862 r_mcbond_other 0.862 r_chiral_restr 0.093 r_gen_planes_refined 0.023 r_gen_planes_other 0.019 r_bond_refined_d 0.009 r_bond_other_d 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6870 Nucleic Acid Atoms Solvent Atoms 1272 Heterogen Atoms 144
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing