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IDOL RING domain in complex with PCM-0102126-001
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 2.12 42.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.267 α = 90 b = 48.053 β = 90.974 c = 70.466 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 2026-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9155 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 1.535 39.699 60.3 0.174 0.198 0.091 0.99 7 4.7 26831
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 1.535 1.695 13.9 1.245 1.408 0.647 0.396 1.6
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 1.535 39.699 26831 1328 60.335 0.179 0.1773 0.1863 0.2144 0.2175 RANDOM 23.139
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] 0.35 0.012 0.062 -0.412
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.555 r_dihedral_angle_3_deg 13.736 r_dihedral_angle_2_deg 9.58 r_lrange_it 8.816 r_lrange_other 8.784 r_scangle_it 6.865 r_scangle_other 6.863 r_dihedral_angle_1_deg 6.849 r_scbond_it 4.312 r_scbond_other 4.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.555 r_dihedral_angle_3_deg 13.736 r_dihedral_angle_2_deg 9.58 r_lrange_it 8.816 r_lrange_other 8.784 r_scangle_it 6.865 r_scangle_other 6.863 r_dihedral_angle_1_deg 6.849 r_scbond_it 4.312 r_scbond_other 4.31 r_mcangle_other 3.435 r_mcangle_it 3.433 r_mcbond_it 2.333 r_mcbond_other 2.332 r_angle_refined_deg 1.503 r_angle_other_deg 0.492 r_symmetry_xyhbond_nbd_refined 0.214 r_nbd_refined 0.205 r_symmetry_nbd_other 0.196 r_xyhbond_nbd_refined 0.196 r_nbd_other 0.182 r_symmetry_nbd_refined 0.167 r_nbtor_refined 0.164 r_ncsr_local_group_6 0.139 r_ncsr_local_group_2 0.133 r_ncsr_local_group_3 0.121 r_ncsr_local_group_4 0.119 r_ncsr_local_group_1 0.114 r_ncsr_local_group_5 0.091 r_metal_ion_refined 0.085 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.076 r_dihedral_angle_other_2_deg 0.055 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 257 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing