5T8Q | pdb_00005t8q

Crystal structure of murine NF-kappaB inducing kinase (NIK) bound to aryl pyrrole fragment 17


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
3.3363.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 143.969α = 90
b = 143.969β = 90
c = 46.455γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2011-02-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9173DiamondI04-1

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
12.6328.7998.50.07416.65.928412
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)
12.632.7689.40.6624.7

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 DIFFRACTIONTHROUGHOUT2.6328.7925565295398.810.203250.197960.20.250240.25RANDOM59.944
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]
-0.07-0.070.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.644
r_dihedral_angle_3_deg16.946
r_dihedral_angle_4_deg15.353
r_dihedral_angle_1_deg6.831
r_long_range_B_refined5.002
r_long_range_B_other5.001
r_scangle_other2.389
r_mcangle_it2.24
r_mcangle_other2.24
r_angle_refined_deg1.601
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.644
r_dihedral_angle_3_deg16.946
r_dihedral_angle_4_deg15.353
r_dihedral_angle_1_deg6.831
r_long_range_B_refined5.002
r_long_range_B_other5.001
r_scangle_other2.389
r_mcangle_it2.24
r_mcangle_other2.24
r_angle_refined_deg1.601
r_scbond_it1.51
r_scbond_other1.51
r_mcbond_it1.334
r_mcbond_other1.328
r_angle_other_deg0.999
r_chiral_restr0.086
r_bond_refined_d0.012
r_gen_planes_refined0.006
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 Atoms5060
Nucleic Acid Atoms
Solvent Atoms71
Heterogen Atoms87

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing