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IDOL RING domain in complex with Z1213725191
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9SA2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.9 293 100 mM sodium phosphate citrate, 4% PEG 400, 4% PEG 500 MME, 4% PEG 600, 4% PEG 1000
Crystal Properties Matthews coefficient Solvent content 2.11 41.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.284 α = 90 b = 47.921 β = 91.107 c = 70.131 γ = 90
Symmetry Space Group P 1 21 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 XE 9M 2026-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9156 Diamond I04-1
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 1.225 39.595 64.8 0.078 0.085 0.033 0.991 11.1 6.2 55983
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 1.225 1.386 6.2 0.537 0.639 0.335 0.711 1.6 3.4
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.225 39.595 55983 1940 64.754 0.138 0.1366 0.1366 0.1793 0.1796 RANDOM 22.132
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] 0.529 0.377 -0.269 -0.274
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 19.859 r_lrange_other 19.517 r_dihedral_angle_6_deg 16.147 r_scangle_it 14.598 r_scangle_other 14.594 r_dihedral_angle_3_deg 10.592 r_scbond_it 9.698 r_scbond_other 9.694 r_mcangle_other 8.836 r_mcangle_it 8.825
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 19.859 r_lrange_other 19.517 r_dihedral_angle_6_deg 16.147 r_scangle_it 14.598 r_scangle_other 14.594 r_dihedral_angle_3_deg 10.592 r_scbond_it 9.698 r_scbond_other 9.694 r_mcangle_other 8.836 r_mcangle_it 8.825 r_dihedral_angle_2_deg 7.62 r_dihedral_angle_1_deg 6.197 r_mcbond_it 5.973 r_mcbond_other 5.943 r_rigid_bond_restr 4.013 r_angle_refined_deg 1.527 r_angle_other_deg 0.512 r_xyhbond_nbd_refined 0.217 r_nbd_refined 0.212 r_symmetry_nbd_other 0.195 r_symmetry_xyhbond_nbd_refined 0.189 r_nbtor_refined 0.167 r_nbd_other 0.166 r_symmetry_nbd_refined 0.141 r_symmetry_xyhbond_nbd_other 0.119 r_ncsr_local_group_6 0.117 r_ncsr_local_group_3 0.114 r_ncsr_local_group_1 0.11 r_ncsr_local_group_4 0.108 r_metal_ion_refined 0.102 r_ncsr_local_group_5 0.09 r_ncsr_local_group_2 0.087 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2159 Nucleic Acid Atoms Solvent Atoms 264 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing