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NF-kappaB RelA homo-dimer bound to GC-centric kappaB DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RAM 2RAM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 PEG3350, MES, Spermine, beta-octylglucoside
Crystal Properties Matthews coefficient Solvent content 2.34 47.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.263 α = 90 b = 133.084 β = 90 c = 45.67 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 2013-11-04 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 1.87 30 99.5 0.987 9.6 6.8 60489
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 1.87 1.9 99.8 3.696 5.8
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 1.87 29.82 56382 2947 97.21 0.15729 0.15364 0.1682 0.22729 0.2343 RANDOM 28.033
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] 0.11 -0.01 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.313 r_dihedral_angle_2_deg 13.604 r_long_range_B_other 9.427 r_long_range_B_refined 9.386 r_scangle_other 9.103 r_dihedral_angle_1_deg 7.602 r_scbond_it 6.877 r_scbond_other 6.86 r_mcangle_other 4.708 r_mcangle_it 4.698
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.313 r_dihedral_angle_2_deg 13.604 r_long_range_B_other 9.427 r_long_range_B_refined 9.386 r_scangle_other 9.103 r_dihedral_angle_1_deg 7.602 r_scbond_it 6.877 r_scbond_other 6.86 r_mcangle_other 4.708 r_mcangle_it 4.698 r_rigid_bond_restr 4.304 r_mcbond_other 3.821 r_mcbond_it 3.82 r_angle_refined_deg 1.676 r_angle_other_deg 0.567 r_chiral_restr 0.098 r_bond_other_d 0.011 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_gen_planes_other 0.002 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 4373 Nucleic Acid Atoms 781 Solvent Atoms 564 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction MOLREP phasing