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IDOL RING domain in complex with PCM-0102246-001
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 2.13 42.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.3 α = 90 b = 48.089 β = 90.917 c = 70.51 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 2026-05-20 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 1.478 29.708 73 0.136 0.15 0.057 0.996 6.6 6.6 36383
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 1.478 1.606 17.5 1.003 1.094 0.429 0.591 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 1.478 29.726 36383 1673 72.973 0.199 0.1968 0.2041 0.2354 0.2386 RANDOM 23.293
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] 0.243 -0.005 -0.037 -0.206
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_2_deg 21.767 r_dihedral_angle_6_deg 14.036 r_dihedral_angle_3_deg 13.184 r_dihedral_angle_2_deg 8.081 r_lrange_other 7.536 r_lrange_it 7.528 r_dihedral_angle_1_deg 6.283 r_scangle_it 5.464 r_scangle_other 5.462 r_scbond_it 3.715
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_2_deg 21.767 r_dihedral_angle_6_deg 14.036 r_dihedral_angle_3_deg 13.184 r_dihedral_angle_2_deg 8.081 r_lrange_other 7.536 r_lrange_it 7.528 r_dihedral_angle_1_deg 6.283 r_scangle_it 5.464 r_scangle_other 5.462 r_scbond_it 3.715 r_scbond_other 3.713 r_mcangle_it 3.18 r_mcangle_other 3.179 r_mcbond_it 2.089 r_mcbond_other 2.079 r_angle_refined_deg 1.41 r_angle_other_deg 0.435 r_symmetry_nbd_refined 0.214 r_nbd_refined 0.2 r_symmetry_nbd_other 0.195 r_xyhbond_nbd_refined 0.186 r_nbd_other 0.167 r_nbtor_refined 0.164 r_symmetry_xyhbond_nbd_refined 0.153 r_ncsr_local_group_6 0.137 r_ncsr_local_group_2 0.121 r_ncsr_local_group_3 0.119 r_ncsr_local_group_4 0.117 r_metal_ion_refined 0.11 r_ncsr_local_group_1 0.104 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.066 r_ncsr_local_group_5 0.064 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2142 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing