5T8O | pdb_00005t8o

Crystal structure of murine NF-kappaB inducing kinase (NIK) bound to Imidazobenzoxepin Compound 3


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.22770.3-0.9M ammonium sulphate, 0.05-0.1M sodium citrate, 0.7-1.0M Lithium sulphate
Crystal Properties
Matthews coefficientSolvent content
3.0659.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 143.95α = 90
b = 143.95β = 90
c = 45.47γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2011-03-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.4150.8995.10.0897.52.5345952
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.412.54950.39422.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.41143.9531025354994.350.206820.201450.20.255660.26RANDOM36.962
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]
0.080.08-0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.963
r_dihedral_angle_4_deg17.682
r_dihedral_angle_3_deg15.209
r_dihedral_angle_1_deg6.284
r_long_range_B_refined3.484
r_long_range_B_other3.41
r_angle_refined_deg1.373
r_angle_other_deg0.937
r_mcangle_it0.784
r_mcangle_other0.784
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.963
r_dihedral_angle_4_deg17.682
r_dihedral_angle_3_deg15.209
r_dihedral_angle_1_deg6.284
r_long_range_B_refined3.484
r_long_range_B_other3.41
r_angle_refined_deg1.373
r_angle_other_deg0.937
r_mcangle_it0.784
r_mcangle_other0.784
r_scangle_other0.65
r_mcbond_it0.43
r_mcbond_other0.43
r_scbond_it0.393
r_scbond_other0.393
r_chiral_restr0.07
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5067
Nucleic Acid Atoms
Solvent Atoms286
Heterogen Atoms81

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing