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Crystal structure of AI-designed homodimer MIYEI
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 8.5 277 Morpheus G9: 30.0% w/v 550M_20K; 0.1 M MB3 pH 8.5; 0.1 M MCA
Crystal Properties Matthews coefficient Solvent content 2.28 46.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.093 α = 90 b = 53.473 β = 112.443 c = 55.786 γ = 90
Symmetry Space Group C 1 2 1
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 CdTe 16M 2025-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.8856 ESRF ID23-1
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 1.773 36.155 99.9 0.0987 0.1066 0.0399 0.997 9.46 6.92 14102
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) 1.773 1.803 99.6 1.1616 1.2633 0.4907 0.688 1.43 6.48 713
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 1.773 36.155 14102 700 99.915 0.192 0.1894 0.1975 0.245 0.2567 37.01
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] -1.157 1.944 -1.832 1.031
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.356 r_dihedral_angle_3_deg 11.372 r_lrange_it 6.542 r_lrange_other 6.49 r_dihedral_angle_1_deg 6.194 r_scangle_it 4.906 r_scangle_other 4.903 r_mcangle_it 3.832 r_mcangle_other 3.832 r_scbond_it 3.197
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.356 r_dihedral_angle_3_deg 11.372 r_lrange_it 6.542 r_lrange_other 6.49 r_dihedral_angle_1_deg 6.194 r_scangle_it 4.906 r_scangle_other 4.903 r_mcangle_it 3.832 r_mcangle_other 3.832 r_scbond_it 3.197 r_scbond_other 3.194 r_mcbond_it 2.572 r_mcbond_other 2.568 r_angle_refined_deg 1.355 r_dihedral_angle_2_deg 0.565 r_angle_other_deg 0.496 r_nbd_refined 0.201 r_symmetry_nbd_other 0.18 r_nbtor_refined 0.151 r_nbd_other 0.146 r_xyhbond_nbd_refined 0.118 r_symmetry_xyhbond_nbd_refined 0.117 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.058 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_symmetry_nbd_refined 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1120 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms
Software Software Software Name Purpose autoPROC data processing Aimless data scaling TRUNCATE data processing REFMAC refinement XDS data reduction PHASER phasing