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Crystal structure of the AGR2 and IRE1beta_loop complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-O95994-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 0.2M Magnesium chloride, 0.1M TRIS PH8.5 and 24% PEG8000
Crystal Properties Matthews coefficient Solvent content 2.19 43.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.199 α = 90 b = 81.82 β = 90 c = 120.871 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER2 X 16M 2024-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.9 67.76 99.6 0.198 0.992 6 6.4 57731
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 1.234 0.707
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.9 67.76 54791 2862 99.57 0.20116 0.19948 0.2062 0.2341 0.2424 RANDOM 21.997
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] -1.86 3.72 -1.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.423 r_dihedral_angle_1_deg 6.741 r_dihedral_angle_2_deg 5.928 r_long_range_B_refined 4.249 r_long_range_B_other 4.175 r_scangle_other 2.91 r_mcangle_it 2.178 r_mcangle_other 2.178 r_scbond_it 1.743 r_scbond_other 1.743
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.423 r_dihedral_angle_1_deg 6.741 r_dihedral_angle_2_deg 5.928 r_long_range_B_refined 4.249 r_long_range_B_other 4.175 r_scangle_other 2.91 r_mcangle_it 2.178 r_mcangle_other 2.178 r_scbond_it 1.743 r_scbond_other 1.743 r_mcbond_it 1.289 r_mcbond_other 1.289 r_angle_refined_deg 1.246 r_angle_other_deg 0.454 r_chiral_restr 0.061 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4789 Nucleic Acid Atoms Solvent Atoms 369 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing