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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 0.32 M Lithium chloride, 0.1 M Sodium citrate pH 5.5, 14 % w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.33 47.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.383 α = 90 b = 149.928 β = 95.632 c = 88.138 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 0.900 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 2.35 43.86 98.3 0.07 0.083 0.045 0.997 9.3 3.4 45799
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 2.35 2.43 99.9 0.851 1.015 0.549 0.613 1.5 3.3
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 2.35 37.854 45759 2367 98.223 0.248 0.2452 0.2451 0.2964 0.2964 63.532
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] -0.026 0.061 -0.01 0.024
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.51 r_dihedral_angle_3_deg 16.16 r_dihedral_angle_4_deg 14.693 r_lrange_it 5.629 r_dihedral_angle_1_deg 3.9 r_scangle_it 2.873 r_mcangle_it 2.4 r_scbond_it 1.686 r_mcbond_it 1.399 r_angle_refined_deg 0.682
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.51 r_dihedral_angle_3_deg 16.16 r_dihedral_angle_4_deg 14.693 r_lrange_it 5.629 r_dihedral_angle_1_deg 3.9 r_scangle_it 2.873 r_mcangle_it 2.4 r_scbond_it 1.686 r_mcbond_it 1.399 r_angle_refined_deg 0.682 r_nbtor_refined 0.287 r_nbd_refined 0.165 r_symmetry_nbd_refined 0.155 r_xyhbond_nbd_refined 0.102 r_symmetry_xyhbond_nbd_refined 0.1 r_chiral_restr 0.059 r_bond_refined_d 0.002 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7301 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data reduction Aimless data scaling MOLREP phasing