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Structure of NF-kB p52 homodimer bound to P-Selectin kB DNA fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1A3Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.1M Sodium malonate, pH 4.0, 0.2M CsCl, 5% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.57 52.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.495 α = 90 b = 85.37 β = 90 c = 140.29 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS3 6M 2019-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97852 SSRF BL19U1
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 3 45.63 95.4 0.999 14.3 14 19950
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 3 3.16 98.2 0.767 1.9 14.2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1a3q 3 42.722 19898 973 94.906 0.238 0.236 0.2378 0.2753 0.2765 107.301
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] -0.378 9.796 -9.418
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.349 r_lrange_it 19.595 r_lrange_other 19.595 r_dihedral_angle_3_deg 18.677 r_dihedral_angle_4_deg 16.767 r_mcangle_it 13.045 r_mcangle_other 13.044 r_scangle_it 12.281 r_scangle_other 12.28 r_mcbond_it 8.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.349 r_lrange_it 19.595 r_lrange_other 19.595 r_dihedral_angle_3_deg 18.677 r_dihedral_angle_4_deg 16.767 r_mcangle_it 13.045 r_mcangle_other 13.044 r_scangle_it 12.281 r_scangle_other 12.28 r_mcbond_it 8.32 r_mcbond_other 8.317 r_scbond_it 7.629 r_scbond_other 7.628 r_dihedral_angle_1_deg 7.268 r_angle_refined_deg 1.78 r_angle_other_deg 1.433 r_symmetry_nbd_refined 0.268 r_nbd_other 0.233 r_symmetry_nbd_other 0.222 r_nbd_refined 0.219 r_ncsr_local_group_1 0.209 r_xyhbond_nbd_refined 0.208 r_nbtor_refined 0.186 r_symmetry_xyhbond_nbd_other 0.148 r_ext_dist_refined_d 0.14 r_chiral_restr 0.102 r_symmetry_nbtor_other 0.087 r_symmetry_xyhbond_nbd_refined 0.074 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4634 Nucleic Acid Atoms 713 Solvent Atoms 12 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing