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TA-centric NF-kappaB RelA binding DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8GAX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 PEG3350 8%, Sodium Acetate pH 3.5 100 mM, 50 mM Zinc Acetate
Crystal Properties Matthews coefficient Solvent content 2.06 40.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.078 α = 89.9 b = 46.233 β = 89.86 c = 98.646 γ = 60.1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS EIGER X 16M 2021-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3 50 88.9 0.11 12.2 2.6 12092
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.1 94.4 0.625 2.8
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 (Observed) 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 3 30 12083 515 88.81 0.26197 0.25843 0.2562 0.33907 0.3213 RANDOM 44.472
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] 2.1 -0.97 0.63 -0.48 -0.25 -2.41
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 5.475 r_long_range_B_other 5.475 r_mcbond_it 4.281 r_scangle_other 2.417 r_scbond_it 1.96 r_scbond_other 1.96 r_angle_other_deg 1.486 r_angle_refined_deg 0.818 r_chiral_restr 0.052 r_bond_refined_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 5.475 r_long_range_B_other 5.475 r_mcbond_it 4.281 r_scangle_other 2.417 r_scbond_it 1.96 r_scbond_other 1.96 r_angle_other_deg 1.486 r_angle_refined_deg 0.818 r_chiral_restr 0.052 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_it r_mcangle_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 5451 Solvent Atoms 462 Heterogen Atoms 126
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing