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Cell surface protein YwfG protein complexed with mannose
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 4.42 72.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.312 α = 90 b = 273.164 β = 90 c = 322.789 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 2019-05-15 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 3 48.71 100 0.145 0.151 0.042 0.998 16 6.8 39549
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 3 3.16 100 1.053 1.097 0.304 0.806 2.7 6.7
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 3 45.569 39421 1964 99.628 0.23 0.2271 0.2314 0.2955 0.2922 79.915
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] 0.021 -0.086 0.065
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 46.434 r_dihedral_angle_4_deg 22.122 r_dihedral_angle_3_deg 21.523 r_lrange_other 18.644 r_lrange_it 18.63 r_scangle_it 16.882 r_scangle_other 16.286 r_mcangle_it 15.25 r_mcangle_other 15.25 r_scbond_it 12.625
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 46.434 r_dihedral_angle_4_deg 22.122 r_dihedral_angle_3_deg 21.523 r_lrange_other 18.644 r_lrange_it 18.63 r_scangle_it 16.882 r_scangle_other 16.286 r_mcangle_it 15.25 r_mcangle_other 15.25 r_scbond_it 12.625 r_scbond_other 11.972 r_mcbond_it 11.491 r_mcbond_other 11.484 r_dihedral_angle_1_deg 7.695 r_angle_refined_deg 2.279 r_angle_other_deg 1.437 r_metal_ion_refined 0.385 r_nbd_other 0.26 r_symmetry_xyhbond_nbd_refined 0.242 r_nbd_refined 0.22 r_symmetry_nbd_other 0.213 r_nbtor_refined 0.188 r_symmetry_nbd_refined 0.182 r_xyhbond_nbd_refined 0.167 r_symmetry_nbtor_other 0.089 r_chiral_restr 0.088 r_symmetry_xyhbond_nbd_other 0.087 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6446 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 163
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling REFMAC phasing