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Plant membrane receptor IGP1 in complex with cellotriose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold C0LGH4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 292.15 100 mM Sodium acetate pH 4.6,
200 mM Ammonium sulfate,
30 % w/v PEG 2000
Crystal Properties Matthews coefficient Solvent content 2.98 58.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.775 α = 90 b = 83.775 β = 90 c = 198.935 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 EIGER X 16M 2023-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.033286 SLS X06SA
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 2.16 48.95 100 0.12 0.138 0.069 0.998 10 7.8 42267 45.37
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) 2.16 2.23 100 2.067 2.474 1.336 0.316 1 6.5
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 2.16 48.95 42194 2076 99.983 0.171 0.169 0.1748 0.2105 0.2128 51.647
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] 0.537 0.269 0.537 -1.743
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.677 r_dihedral_angle_3_deg 14.162 r_dihedral_angle_2_deg 8.887 r_lrange_other 8.629 r_lrange_it 8.626 r_scangle_it 8.318 r_scangle_other 8.28 r_dihedral_angle_1_deg 7.63 r_scbond_it 6.152 r_scbond_other 6.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.677 r_dihedral_angle_3_deg 14.162 r_dihedral_angle_2_deg 8.887 r_lrange_other 8.629 r_lrange_it 8.626 r_scangle_it 8.318 r_scangle_other 8.28 r_dihedral_angle_1_deg 7.63 r_scbond_it 6.152 r_scbond_other 6.112 r_mcangle_it 5.35 r_mcangle_other 5.349 r_dihedral_angle_other_1_deg 4.439 r_mcbond_it 3.807 r_mcbond_other 3.806 r_angle_refined_deg 2.289 r_angle_other_deg 0.774 r_nbd_other 0.231 r_nbd_refined 0.218 r_symmetry_nbd_other 0.21 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.145 r_symmetry_nbd_refined 0.141 r_chiral_restr 0.104 r_symmetry_nbtor_other 0.096 r_symmetry_xyhbond_nbd_refined 0.081 r_metal_ion_refined 0.072 r_symmetry_xyhbond_nbd_other 0.025 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4448 Nucleic Acid Atoms Solvent Atoms 188 Heterogen Atoms 312
Software Software Software Name Purpose REFMAC refinement pointless data scaling Aimless data scaling Coot model building PHENIX phasing