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Outer membrane lipoprotein QseG of Escherichia coli O157:H7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.08 M magnesium acetate tetrahydrate, 0.1 M sodium citrate pH 6.0, 14% (w/v) polyethylene glycol monomethyl ether 5000
Crystal Properties Matthews coefficient Solvent content 2.31 46.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.963 α = 90 b = 149.785 β = 94.649 c = 88.302 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2021-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9000 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.3 43.43 98.9 0.091 0.108 0.058 0.996 8.5 3.4 48807
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 99.7 0.834 0.983 0.516 0.65 1.6 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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE AlphaFold structure 2.3 39.803 48774 2466 98.839 0.223 0.2206 0.2735 0.2853 52.887
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] -0.095 -0.031 -0.006 0.105
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.122 r_dihedral_angle_3_deg 21.163 r_dihedral_angle_4_deg 20.35 r_lrange_it 9.305 r_scangle_it 9.106 r_scbond_it 7.534 r_mcangle_it 6.625 r_mcbond_it 5.606 r_dihedral_angle_1_deg 5.332 r_angle_refined_deg 1.513
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.122 r_dihedral_angle_3_deg 21.163 r_dihedral_angle_4_deg 20.35 r_lrange_it 9.305 r_scangle_it 9.106 r_scbond_it 7.534 r_mcangle_it 6.625 r_mcbond_it 5.606 r_dihedral_angle_1_deg 5.332 r_angle_refined_deg 1.513 r_nbtor_refined 0.315 r_xyhbond_nbd_refined 0.245 r_symmetry_xyhbond_nbd_refined 0.231 r_nbd_refined 0.23 r_symmetry_nbd_refined 0.206 r_chiral_restr 0.065 r_metal_ion_refined 0.019 r_bond_refined_d 0.01 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7281 Nucleic Acid Atoms Solvent Atoms 279 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data reduction Aimless data scaling MOLREP phasing