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Escherichia coli OpgG mutant-D361N with beta-1,2-glucan
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TXK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 MMT (pH 5.0), PEG400
Crystal Properties Matthews coefficient Solvent content 2.3 46.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.821 α = 90 b = 80.97 β = 90 c = 213.225 γ = 90
Symmetry Space Group C 2 2 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 PILATUS3 S 6M 2021-07-04 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 1.81 48.34 99.9 0.999 17.2 6.4 50021
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 1.81 1.85 0.891
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.81 48.34 49959 2535 99.876 0.215 0.2134 0.2178 0.254 0.254 41.948
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] -0.123 -0.075 0.198
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.452 r_dihedral_angle_4_deg 18.251 r_dihedral_angle_3_deg 15.08 r_rigid_bond_restr 13.057 r_dihedral_angle_1_deg 7.457 r_angle_other_deg 3.379 r_angle_refined_deg 1.719 r_lrange_other 0.723 r_lrange_it 0.721 r_mcangle_other 0.498
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.452 r_dihedral_angle_4_deg 18.251 r_dihedral_angle_3_deg 15.08 r_rigid_bond_restr 13.057 r_dihedral_angle_1_deg 7.457 r_angle_other_deg 3.379 r_angle_refined_deg 1.719 r_lrange_other 0.723 r_lrange_it 0.721 r_mcangle_other 0.498 r_mcangle_it 0.491 r_scangle_it 0.482 r_scangle_other 0.482 r_mcbond_other 0.294 r_scbond_it 0.286 r_scbond_other 0.286 r_mcbond_it 0.28 r_nbd_other 0.239 r_symmetry_nbd_other 0.23 r_nbd_refined 0.201 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.148 r_symmetry_xyhbond_nbd_refined 0.146 r_symmetry_nbd_refined 0.142 r_symmetry_nbtor_other 0.115 r_chiral_restr 0.098 r_bond_other_d 0.034 r_symmetry_xyhbond_nbd_other 0.025 r_gen_planes_other 0.016 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_xyhbond_nbd_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3819 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 177
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing