7OK6

Crystal structure of UNC119B in complex with LCK peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6H6A 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29130 % w/v PEG 4,000, 0.1 M HEPES pH 7.5, 0.2 M CaCl2
Crystal Properties
Matthews coefficientSolvent content
2.448.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.083α = 90
b = 67.004β = 90
c = 106.691γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-09-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91589DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.94956.74299.70.99812.76.429562
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)
11.94920.91

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6H6A1.94956.74229499147799.8650.1840.18150.223932.072
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]
-1.9633.657-1.693
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.408
r_dihedral_angle_4_deg17.012
r_dihedral_angle_3_deg15.888
r_lrange_it7.242
r_lrange_other7.227
r_dihedral_angle_1_deg7.087
r_scangle_it5.402
r_scangle_other5.401
r_mcangle_it4.067
r_mcangle_other4.066
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.408
r_dihedral_angle_4_deg17.012
r_dihedral_angle_3_deg15.888
r_lrange_it7.242
r_lrange_other7.227
r_dihedral_angle_1_deg7.087
r_scangle_it5.402
r_scangle_other5.401
r_mcangle_it4.067
r_mcangle_other4.066
r_scbond_it3.512
r_scbond_other3.512
r_mcbond_it2.734
r_mcbond_other2.733
r_angle_refined_deg1.594
r_angle_other_deg1.29
r_nbd_refined0.202
r_symmetry_nbd_other0.202
r_nbd_other0.199
r_symmetry_nbd_refined0.178
r_nbtor_refined0.173
r_xyhbond_nbd_refined0.15
r_symmetry_xyhbond_nbd_refined0.137
r_symmetry_nbtor_other0.091
r_chiral_restr0.083
r_metal_ion_refined0.065
r_symmetry_xyhbond_nbd_other0.058
r_symmetry_metal_ion_refined0.042
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2862
Nucleic Acid Atoms
Solvent Atoms177
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing