8TKN

Murine NF-kappaB p50 Rel Homology Region homodimer in complex with 10-mer kappaB DNA from human Neutrophil Gelatinase-associated Lipocalin (NGAL) promoter


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NFK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.42980.05 M sodium acetate pH 5.4, 20 mM magnesium sulfate, and 4% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.6854.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.006α = 90
b = 102.644β = 90
c = 127.704γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-10-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.10.99999ALS8.2.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.8501000.0831962312374.81
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.850.7642.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1NFK2.847.621.3421798112597.60.24130.23880.287881.31
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d17.9371
f_angle_d0.5851
f_chiral_restr0.0418
f_plane_restr0.0047
f_bond_d0.0037
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4906
Nucleic Acid Atoms806
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
HKL-2000data collection
autoPROCdata processing
PHENIXmodel building
PHENIXrefinement