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X-ray structure of a NF-kB p50-RelB-DNA complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VKX PDB ENTRY 1VKX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 5% PEG3350 100 MM NACITRATE 1MM SPERMINE 5MM DTT, pH 7
Crystal Properties Matthews coefficient Solvent content 3.34 65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.44 α = 90 b = 91.44 β = 90 c = 419.97 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 105 CCD ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 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 3.04 30 96 0.06 12 12.8 19931 86
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 3.04 3.15 91 0.51 2.5 9.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1VKX 3.05 19.9 2 19087 916 91.6 0.238 0.238 0.276 RANDOM 74
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] 10.87 20.2 10.87 -21.74
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.6 c_angle_deg 1.4 c_improper_angle_d 1.13 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.6 c_angle_deg 1.4 c_improper_angle_d 1.13 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4658 Nucleic Acid Atoms 442 Solvent Atoms 34 Heterogen Atoms
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing