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Investigating the binding mechanism of Interferon Regulatory Factor 4 to DNA in the context of Multiple Myeloma
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB PDB_00007OOT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 0.2M Calcium Acetate, 0.1M MES pH 6, 20% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.77 55.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.512 α = 89.859 b = 65.116 β = 75.316 c = 70.694 γ = 66.791
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 16M 2025-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
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 1.86 59.556 95.52 0.9757 11.14 3.6 70231
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 1.86 1.89 0.363
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 2.1 59.556 50135 1471 98.192 0.212 0.2107 0.2113 0.2578 0.2581 55.671
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] 6.724 0.12 -4.069 -4.995 0.131 -2.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.877 r_lrange_other 15.586 r_lrange_it 15.575 r_dihedral_angle_6_deg 15.052 r_scangle_it 11.962 r_scangle_other 11.961 r_dihedral_angle_2_deg 10.681 r_mcangle_it 9.853 r_mcangle_other 9.851 r_scbond_it 9.634
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.877 r_lrange_other 15.586 r_lrange_it 15.575 r_dihedral_angle_6_deg 15.052 r_scangle_it 11.962 r_scangle_other 11.961 r_dihedral_angle_2_deg 10.681 r_mcangle_it 9.853 r_mcangle_other 9.851 r_scbond_it 9.634 r_scbond_other 9.634 r_mcbond_it 8.011 r_mcbond_other 7.99 r_dihedral_angle_1_deg 7.469 r_angle_refined_deg 2.877 r_angle_other_deg 0.845 r_dihedral_angle_other_2_deg 0.815 r_symmetry_xyhbond_nbd_refined 0.34 r_nbd_other 0.244 r_nbd_refined 0.224 r_symmetry_nbd_refined 0.22 r_symmetry_nbd_other 0.217 r_nbtor_refined 0.217 r_xyhbond_nbd_refined 0.19 r_chiral_restr 0.126 r_ncsr_local_group_1 0.123 r_ncsr_local_group_4 0.119 r_ncsr_local_group_3 0.114 r_ncsr_local_group_8 0.111 r_symmetry_nbtor_other 0.098 r_ncsr_local_group_5 0.095 r_metal_ion_refined 0.084 r_ncsr_local_group_2 0.064 r_ncsr_local_group_6 0.05 r_ncsr_local_group_7 0.049 r_symmetry_xyhbond_nbd_other 0.043 r_gen_planes_refined 0.018 r_bond_refined_d 0.015 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3749 Nucleic Acid Atoms 1640 Solvent Atoms 107 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing