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CG-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 293 PEG3350 8%, Sodium Acetate pH 3.5 100 mM, 50 mM Zinc Acetate
Crystal Properties Matthews coefficient Solvent content 2.14 42.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.999 α = 90.03 b = 47.031 β = 89.96 c = 98.682 γ = 59.99
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 2.6 50 92 0.08 15 3.7 20414
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 2.6 2.69 95.6 0.35 2.9 3.8
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 2.6 30 19780 961 92.36 0.30072 0.29833 0.2976 0.34887 0.3428 RANDOM 44.479
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] 0.31 0.21 0.79 -0.08 -0.2 0.06
RMS Deviations Key Refinement Restraint Deviation r_mcbond_it 5.237 r_long_range_B_refined 4.797 r_long_range_B_other 4.797 r_scangle_other 2.624 r_scbond_it 2.387 r_scbond_other 2.387 r_angle_other_deg 1.44 r_angle_refined_deg 0.767 r_chiral_restr 0.05 r_bond_refined_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_mcbond_it 5.237 r_long_range_B_refined 4.797 r_long_range_B_other 4.797 r_scangle_other 2.624 r_scbond_it 2.387 r_scbond_other 2.387 r_angle_other_deg 1.44 r_angle_refined_deg 0.767 r_chiral_restr 0.05 r_bond_refined_d 0.007 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 474 Heterogen Atoms 127
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling SHELX phasing