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Cell surface protein YwfG protein complexed with alpha-1,2-mannobiose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7YL4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M sodium acetate (pH 5.0-5.6),
1.3 M Li2SO4,
2% (w/v) polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 4.37 71.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.454 α = 90 b = 276.634 β = 90 c = 321.75 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 PIXEL DECTRIS PILATUS3 S 2M 2020-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
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 2.95 43.06 99.9 0.203 0.211 0.058 0.996 14 13 42029
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 2.95 3.11 1.187 1.232 0.329 0.774 2.5
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 FOURIER SYNTHESIS FREE R-VALUE 7YL4 2.95 41.511 42023 2151 99.888 0.214 0.2114 0.2173 0.2684 0.2699 65.208
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] -1.638 1.913 -0.276
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.927 r_dihedral_angle_3_deg 21.631 r_dihedral_angle_4_deg 18.724 r_lrange_it 13.987 r_lrange_other 13.962 r_scangle_it 12.238 r_scangle_other 12.046 r_mcangle_it 10.738 r_mcangle_other 10.738 r_scbond_it 8.476
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.927 r_dihedral_angle_3_deg 21.631 r_dihedral_angle_4_deg 18.724 r_lrange_it 13.987 r_lrange_other 13.962 r_scangle_it 12.238 r_scangle_other 12.046 r_mcangle_it 10.738 r_mcangle_other 10.738 r_scbond_it 8.476 r_scbond_other 8.322 r_mcbond_it 7.546 r_mcbond_other 7.539 r_dihedral_angle_1_deg 6.875 r_angle_refined_deg 2.033 r_angle_other_deg 1.406 r_metal_ion_refined 0.358 r_nbd_refined 0.212 r_nbd_other 0.21 r_symmetry_nbd_other 0.209 r_symmetry_nbd_refined 0.196 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.157 r_symmetry_xyhbond_nbd_other 0.091 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.071 r_symmetry_xyhbond_nbd_refined 0.045 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6534 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 98
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling REFMAC phasing