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Structure of NF-kB p52 homodimer bound to +1/-1 swap 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, SITTING DROP 293 0.1M Sodium malonate, pH 4.0, 50mM CsCl, 2.5% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.53 51.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.987 α = 90 b = 84.289 β = 90 c = 140.565 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 93 PIXEL DECTRIS EIGER X 16M 2019-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.979183 SSRF BL17U1
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 3.4 46.85 99.7 0.998 9.6 13 14272
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 3.4 3.58 0.782
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 3.4 45.451 14233 690 99.699 0.272 0.2712 0.2706 0.2858 0.2829 156.456
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] 15.984 2.19 -18.174
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.02 r_lrange_it 25.429 r_lrange_other 25.428 r_dihedral_angle_3_deg 18.325 r_mcangle_it 17.231 r_mcangle_other 17.229 r_scangle_it 15.361 r_scangle_other 15.359 r_dihedral_angle_4_deg 14.484 r_mcbond_other 10.764
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.02 r_lrange_it 25.429 r_lrange_other 25.428 r_dihedral_angle_3_deg 18.325 r_mcangle_it 17.231 r_mcangle_other 17.229 r_scangle_it 15.361 r_scangle_other 15.359 r_dihedral_angle_4_deg 14.484 r_mcbond_other 10.764 r_mcbond_it 10.762 r_scbond_it 9.381 r_scbond_other 9.381 r_dihedral_angle_1_deg 7.722 r_angle_refined_deg 1.735 r_angle_other_deg 1.328 r_symmetry_xyhbond_nbd_refined 0.706 r_xyhbond_nbd_other 0.509 r_symmetry_nbd_refined 0.324 r_nbd_other 0.305 r_symmetry_nbd_other 0.21 r_nbd_refined 0.205 r_xyhbond_nbd_refined 0.194 r_nbtor_refined 0.184 r_ncsr_local_group_1 0.119 r_chiral_restr 0.115 r_ext_dist_refined_d 0.094 r_symmetry_nbtor_other 0.085 r_symmetry_xyhbond_nbd_other 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4668 Nucleic Acid Atoms 691 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing