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Plant membrane receptor IGP1
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 0.1 M Sodium acetate trihydrate pH 4.6
0.2 M Ammonium sulfate
30 % PEG 2000
Crystal Properties Matthews coefficient Solvent content 3 59.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.365 α = 90 b = 84.365 β = 90 c = 198.32 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 2023-09-20 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 2.62 49.58 100 0.428 0.475 0.205 0.973 5.9 10.5 24021
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) 2.62 2.74 100 2.114 2.412 1.147 0.314 1 8.7
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 2.62 49.068 23962 1185 99.987 0.186 0.1823 0.1895 0.2564 0.2577 36.261
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] 0.442 0.221 0.442 -1.434
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.309 r_dihedral_angle_6_deg 15.124 r_dihedral_angle_2_deg 12.944 r_dihedral_angle_1_deg 7.748 r_lrange_other 6.817 r_lrange_it 6.804 r_scangle_it 5.973 r_scangle_other 5.838 r_mcangle_it 4 r_mcangle_other 4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.309 r_dihedral_angle_6_deg 15.124 r_dihedral_angle_2_deg 12.944 r_dihedral_angle_1_deg 7.748 r_lrange_other 6.817 r_lrange_it 6.804 r_scangle_it 5.973 r_scangle_other 5.838 r_mcangle_it 4 r_mcangle_other 4 r_scbond_it 3.974 r_scbond_other 3.824 r_mcbond_it 2.521 r_mcbond_other 2.517 r_angle_refined_deg 2.335 r_angle_other_deg 0.788 r_symmetry_nbd_other 0.22 r_nbd_other 0.218 r_nbd_refined 0.215 r_nbtor_refined 0.188 r_symmetry_xyhbond_nbd_refined 0.169 r_xyhbond_nbd_refined 0.159 r_symmetry_nbd_refined 0.147 r_symmetry_xyhbond_nbd_other 0.121 r_chiral_restr 0.102 r_symmetry_nbtor_other 0.095 r_metal_ion_refined 0.082 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4479 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 264
Software Software Software Name Purpose REFMAC refinement pointless data scaling Aimless data scaling Coot model building PHENIX phasing