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Crystal structure of AfRIOK1 and the inhibitor CINS-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.5 M Lithium sulfate monohydrate, 0.1 M Sodium acetate trihydrate
Crystal Properties Matthews coefficient Solvent content 3.7 66.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.818 α = 90 b = 138.818 β = 90 c = 138.818 γ = 90
Symmetry Space Group I 21 3
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 S 16M 2023-12-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.97915 SSRF BL10U2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.758 69.41 100 0.986 13.8 1.9 11664
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.76 2.91 0.491
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 2.758 69.409 11657 563 99.914 0.284 0.2823 0.2848 0.3246 0.3228 79.062
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 13.695 r_dihedral_angle_3_deg 12.788 r_dihedral_angle_6_deg 9.558 r_dihedral_angle_1_deg 5.961 r_scangle_it 1.301 r_scangle_other 1.3 r_lrange_it 1.297 r_lrange_other 1.297 r_mcangle_it 1.063 r_mcangle_other 1.062
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 13.695 r_dihedral_angle_3_deg 12.788 r_dihedral_angle_6_deg 9.558 r_dihedral_angle_1_deg 5.961 r_scangle_it 1.301 r_scangle_other 1.3 r_lrange_it 1.297 r_lrange_other 1.297 r_mcangle_it 1.063 r_mcangle_other 1.062 r_scbond_it 1.014 r_scbond_other 1.014 r_mcbond_other 1.002 r_mcbond_it 1.001 r_angle_refined_deg 0.428 r_symmetry_nbd_other 0.24 r_nbd_refined 0.238 r_symmetry_xyhbond_nbd_other 0.233 r_nbd_other 0.226 r_symmetry_nbd_refined 0.221 r_nbtor_refined 0.191 r_angle_other_deg 0.158 r_xyhbond_nbd_refined 0.158 r_symmetry_nbtor_other 0.08 r_symmetry_xyhbond_nbd_refined 0.031 r_chiral_restr 0.024 r_gen_planes_refined 0.012 r_bond_refined_d 0.004 r_gen_planes_other 0.003 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1978 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing