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Xanthomonas campestris pv. campestris OpgD mutant-D379N 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, SITTING DROP 5.5 293 Bis-Tris HCl (pH5.5), Ammonium sulfate, glycerol, beta-1,2-glucan
Crystal Properties Matthews coefficient Solvent content 4.89 74.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 171.878 α = 90 b = 171.878 β = 90 c = 128.691 γ = 120
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 2023-06-10 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 2.25 48.723 100 0.996 11.6 10.4 102253
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 2.25 2.29 0.83
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 2.25 48.723 102207 5213 99.987 0.173 0.1726 0.1807 0.1761 0.1841 31.145
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] -0.632 -0.316 -0.632 2.049
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.316 r_dihedral_angle_6_deg 16.14 r_dihedral_angle_3_deg 15.57 r_lrange_other 7.951 r_lrange_it 7.942 r_dihedral_angle_1_deg 6.977 r_scangle_it 6.37 r_scangle_other 6.369 r_mcangle_it 4.377 r_mcangle_other 4.377
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.316 r_dihedral_angle_6_deg 16.14 r_dihedral_angle_3_deg 15.57 r_lrange_other 7.951 r_lrange_it 7.942 r_dihedral_angle_1_deg 6.977 r_scangle_it 6.37 r_scangle_other 6.369 r_mcangle_it 4.377 r_mcangle_other 4.377 r_scbond_it 4.297 r_scbond_other 4.297 r_mcbond_it 3.042 r_mcbond_other 3.042 r_angle_refined_deg 1.508 r_angle_other_deg 0.837 r_nbd_refined 0.409 r_symmetry_nbd_refined 0.235 r_symmetry_nbd_other 0.229 r_nbd_other 0.197 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.168 r_symmetry_xyhbond_nbd_refined 0.124 r_symmetry_nbtor_other 0.09 r_chiral_restr 0.065 r_symmetry_xyhbond_nbd_other 0.044 r_gen_planes_other 0.012 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7947 Nucleic Acid Atoms Solvent Atoms 541 Heterogen Atoms 524
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing