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NF-kappaB RelA homo-dimer bound to AT-centric kappaB DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RAM partial
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 PEG3350, MES, beta-octylglucoside, spermine
Crystal Properties Matthews coefficient Solvent content 2.24 45.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.516 α = 90 b = 133.568 β = 90 c = 45.443 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 CCD ADSC QUANTUM 315 2013-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9793 APS 19-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 2.03 30 99.7 0.994 6.9 12.1 46270
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 2.03 2.06 99.1 2.32 10.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 2RAM 2.03 28.91 33225 1739 75.34 0.22573 0.22322 0.2304 0.2733 0.2762 RANDOM 35.057
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] -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.022 r_dihedral_angle_1_deg 7.314 r_dihedral_angle_2_deg 4.656 r_rigid_bond_restr 2.627 r_angle_refined_deg 1.204 r_long_range_B_refined 1.167 r_long_range_B_other 1.121 r_angle_other_deg 0.845 r_scangle_other 0.512 r_mcangle_it 0.497
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.022 r_dihedral_angle_1_deg 7.314 r_dihedral_angle_2_deg 4.656 r_rigid_bond_restr 2.627 r_angle_refined_deg 1.204 r_long_range_B_refined 1.167 r_long_range_B_other 1.121 r_angle_other_deg 0.845 r_scangle_other 0.512 r_mcangle_it 0.497 r_mcangle_other 0.497 r_scbond_it 0.428 r_scbond_other 0.424 r_mcbond_it 0.41 r_mcbond_other 0.41 r_chiral_restr 0.078 r_bond_other_d 0.026 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_gen_planes_other 0.004 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_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4384 Nucleic Acid Atoms 781 Solvent Atoms 397 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction MOLREP phasing