6G4Y | pdb_00006g4y

Crystal structure of murine NF-kappaB inducing kinase (NIK) in complex with compound 1a


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
3.0659.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 143.829α = 90
b = 143.829β = 90
c = 45.614γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M-F2012-08-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.65143.810011.96.727695
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.652.78

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 REPLACEMENTTHROUGHOUT2.65143.826274140899.930.198420.195770.20.249140.24RANDOM50.993
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]
-2.64-2.645.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.279
r_dihedral_angle_4_deg15.527
r_dihedral_angle_3_deg14.821
r_dihedral_angle_1_deg5.785
r_long_range_B_refined3.903
r_long_range_B_other3.872
r_mcangle_it1.88
r_mcangle_other1.879
r_scangle_other1.522
r_angle_refined_deg1.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.279
r_dihedral_angle_4_deg15.527
r_dihedral_angle_3_deg14.821
r_dihedral_angle_1_deg5.785
r_long_range_B_refined3.903
r_long_range_B_other3.872
r_mcangle_it1.88
r_mcangle_other1.879
r_scangle_other1.522
r_angle_refined_deg1.309
r_mcbond_it1.02
r_mcbond_other1.02
r_angle_other_deg0.915
r_scbond_it0.823
r_scbond_other0.822
r_chiral_restr0.065
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms5054
Nucleic Acid Atoms
Solvent Atoms83
Heterogen Atoms92

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing