4LJO

Structure of an active ligase (HOIP)/ubiquitin transfer complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4LJQpdb entry 4LJQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.52930.1 M carboxylic acids, 0.1 M imidazole, MES, 30 % P550 MME_P20K, pH 6.5, vapour diffusion, temperature 293K, VAPOR DIFFUSION
Crystal Properties
Matthews coefficientSolvent content
2.4650.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.95α = 90
b = 45.95β = 90
c = 133.01γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.920DiamondI02

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
11.5644.3499.20.03912.23.48881844055-327.559
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.561.6940.5931.52

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTpdb entry 4LJQ1.56444.3370.7344055222094.60.18280.18120.212439.0035
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.877
f_angle_d1.032
f_chiral_restr0.071
f_bond_d0.006
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2306
Nucleic Acid Atoms
Solvent Atoms220
Heterogen Atoms10

Software

Software
Software NamePurpose
PHENIXrefinement
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CCP4refinement
XSCALEdata scaling
CCP4data reduction
CCP4data scaling