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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 0.1 M Magnesium chloride hexahydrate, 0.1 M Tris pH 7.5, 13 % w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.39 48.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.087 α = 90 b = 123.808 β = 90 c = 150.157 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 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 0.900 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 2.6 47.76 99.9 0.11 0.12 0.047 0.997 10.9 6.6 25039
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 2.6 2.72 100 1.317 1.425 0.539 0.749 1.7 6.9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE AlphaFold structure 2.6 35.903 24975 1231 99.816 0.247 0.2448 0.2453 0.2954 0.297 81.29
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] 5.221 -1.351 -3.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.778 r_dihedral_angle_3_deg 17.401 r_dihedral_angle_4_deg 15.738 r_lrange_it 8.015 r_dihedral_angle_1_deg 4.353 r_scangle_it 4.334 r_mcangle_it 3.872 r_scbond_it 2.589 r_mcbond_it 2.273 r_angle_refined_deg 0.711
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.778 r_dihedral_angle_3_deg 17.401 r_dihedral_angle_4_deg 15.738 r_lrange_it 8.015 r_dihedral_angle_1_deg 4.353 r_scangle_it 4.334 r_mcangle_it 3.872 r_scbond_it 2.589 r_mcbond_it 2.273 r_angle_refined_deg 0.711 r_nbtor_refined 0.288 r_nbd_refined 0.181 r_symmetry_nbd_refined 0.149 r_xyhbond_nbd_refined 0.108 r_symmetry_xyhbond_nbd_refined 0.075 r_chiral_restr 0.063 r_bond_refined_d 0.002 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4937 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data reduction Aimless data scaling MOLREP phasing