6G4Z

Crystal structure of murine NF-kappaB inducing kinase (NIK) in complex with compound 2f


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4G3E 

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
3.1761.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 144.83α = 90
b = 144.83β = 90
c = 46.53γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2013-06-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.97949DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
12.8436.2198.10.1040.98111.76.121715
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.842.9199.90.7450.846.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4G3E2.8436.21217151171980.2370.2340.283RANDOM76.77
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]
0.020.02-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.017
r_dihedral_angle_3_deg15.319
r_dihedral_angle_4_deg14.664
r_long_range_B_refined6.092
r_long_range_B_other6.092
r_dihedral_angle_1_deg5.477
r_mcangle_other3.738
r_mcangle_it3.737
r_scangle_other3.631
r_mcbond_it2.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.017
r_dihedral_angle_3_deg15.319
r_dihedral_angle_4_deg14.664
r_long_range_B_refined6.092
r_long_range_B_other6.092
r_dihedral_angle_1_deg5.477
r_mcangle_other3.738
r_mcangle_it3.737
r_scangle_other3.631
r_mcbond_it2.17
r_mcbond_other2.166
r_scbond_it2.111
r_scbond_other2.111
r_angle_refined_deg1.052
r_angle_other_deg0.701
r_chiral_restr0.052
r_bond_refined_d0.005
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 Atoms5020
Nucleic Acid Atoms
Solvent Atoms18
Heterogen Atoms58

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing