5WNK

Crystal structure of murine receptor-interacting protein 4 (Ripk4) D143N bound to TG100-115


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH2920.1M HEPES pH 7.5, 200 mM magnesium chloride, 10% isopropanol, 15% ethylene glycol, 10% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
3.6566.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.769α = 90
b = 110.231β = 90
c = 146.277γ = 90
Symmetry
Space GroupI 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-06-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21.0ALS5.0.2

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
13.1150.0198.30.01399.43.816445

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3.1150.01983954799.050.227710.22510.27248RANDOM83.873
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]
7.320.94-8.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.419
r_dihedral_angle_3_deg14.104
r_dihedral_angle_4_deg11.671
r_long_range_B_refined8.414
r_long_range_B_other8.386
r_scangle_other6.352
r_mcangle_it6.328
r_mcangle_other6.328
r_dihedral_angle_1_deg5.693
r_scbond_it4.031
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.419
r_dihedral_angle_3_deg14.104
r_dihedral_angle_4_deg11.671
r_long_range_B_refined8.414
r_long_range_B_other8.386
r_scangle_other6.352
r_mcangle_it6.328
r_mcangle_other6.328
r_dihedral_angle_1_deg5.693
r_scbond_it4.031
r_scbond_other4.021
r_mcbond_it3.927
r_mcbond_other3.923
r_angle_refined_deg1.219
r_angle_other_deg0.919
r_chiral_restr0.066
r_bond_refined_d0.008
r_gen_planes_refined0.006
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 Atoms2006
Nucleic Acid Atoms
Solvent Atoms2
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing