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Escherichia coli OpgD mutant-D388N with beta-1,2-glucan
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, HANGING DROP 293 MMT (pH 4.0), PEG1500, Beta-1,2-glucan
Crystal Properties Matthews coefficient Solvent content 2.28 46.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.092 α = 90 b = 87.099 β = 101.132 c = 110.853 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 PILATUS3 S 6M 2022-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.06 47.74 99.3 0.996 12.8 6.5 66585
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.06 2.11 0.697
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.06 47.74 66562 3252 99.212 0.178 0.1751 0.224 0.1991 22.845
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] -1.061 -1.133 2.574 -0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.79 r_dihedral_angle_4_deg 19.37 r_dihedral_angle_3_deg 13.956 r_dihedral_angle_1_deg 7.466 r_lrange_other 4.337 r_lrange_it 4.321 r_scangle_it 3.159 r_scangle_other 3.159 r_angle_other_deg 3.138 r_mcangle_it 2.192
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.79 r_dihedral_angle_4_deg 19.37 r_dihedral_angle_3_deg 13.956 r_dihedral_angle_1_deg 7.466 r_lrange_other 4.337 r_lrange_it 4.321 r_scangle_it 3.159 r_scangle_other 3.159 r_angle_other_deg 3.138 r_mcangle_it 2.192 r_mcangle_other 2.192 r_scbond_it 2.024 r_scbond_other 2.024 r_angle_refined_deg 1.597 r_mcbond_it 1.493 r_mcbond_other 1.491 r_nbd_other 0.264 r_symmetry_nbd_other 0.216 r_nbd_refined 0.198 r_nbtor_refined 0.172 r_symmetry_xyhbond_nbd_refined 0.147 r_xyhbond_nbd_refined 0.143 r_symmetry_nbtor_other 0.127 r_symmetry_nbd_refined 0.11 r_symmetry_xyhbond_nbd_other 0.095 r_chiral_restr 0.073 r_bond_other_d 0.034 r_gen_planes_other 0.01 r_bond_refined_d 0.008 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8157 Nucleic Acid Atoms Solvent Atoms 566 Heterogen Atoms 290
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing