7UPM

Tribbles (TRIB2) pseudokinase bound to nanobody Nb4.103


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.62910.2 M Magnesium nitrate hexahydrate, 20% w/v Polyethylene glycol 3350
Crystal Properties
Matthews coefficientSolvent content
2.6954.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.16α = 90
b = 75.16β = 90
c = 273.77γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-02-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.9537Australian SynchrotronMX2

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
12.745.6799.70.1670.99710.26.313514
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.770.502

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 REPLACEMENTTHROUGHOUT5cem2.745.6711150102190.590.206760.201870.25967RANDOM58.447
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]
-0.25-0.13-0.250.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.472
r_long_range_B_other12.697
r_long_range_B_refined12.69
r_dihedral_angle_3_deg12.164
r_dihedral_angle_4_deg10.467
r_scangle_other8.863
r_mcangle_it8.391
r_mcangle_other8.39
r_scbond_it5.626
r_scbond_other5.624
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.472
r_long_range_B_other12.697
r_long_range_B_refined12.69
r_dihedral_angle_3_deg12.164
r_dihedral_angle_4_deg10.467
r_scangle_other8.863
r_mcangle_it8.391
r_mcangle_other8.39
r_scbond_it5.626
r_scbond_other5.624
r_mcbond_it5.375
r_mcbond_other5.354
r_dihedral_angle_1_deg4.889
r_angle_refined_deg0.955
r_angle_other_deg0.902
r_chiral_restr0.051
r_bond_refined_d0.004
r_gen_planes_refined0.002
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2914
Nucleic Acid Atoms
Solvent Atoms40
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing