9QUG | pdb_00009qug

Structure of a UBC-Ubiquitin conjugate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1UBQ 
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.2 M Trimethylamine N-oxide dihydrate, 0.1 M Tris pH 8.5, 20% (w/v) Polyethylene glycol monomethyl ether 2,000
Crystal Properties
Matthews coefficientSolvent content
2.4750.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.577α = 90
b = 82.845β = 90
c = 98.657γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2022-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.99999SLSX10SA

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
11.59664100117.4413.286771232.27
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)
11.5961.6240.1206

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.849.331.3645284229495.350.16820.1670.16710.19160.191845.32
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_d16.5977
f_angle_d1.4952
f_chiral_restr0.1008
f_bond_d0.0176
f_plane_restr0.0132
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2877
Nucleic Acid Atoms
Solvent Atoms192
Heterogen Atoms77

Software

Software
Software NamePurpose
PHENIXrefinement
PHASERphasing
STARANISOdata scaling
XDSdata reduction