4DBG

Crystal structure of HOIL-1L-UBL complexed with a HOIP-UBA derivative


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529315%(w/v) PEG6000, 0.1M KCl, 0.1M HEPES-Na buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
3.2562.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.973α = 90
b = 64.973β = 90
c = 161.291γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker DIP-6040Horizontal focusing mirror2009-02-16MSINGLE WAVELENGTH
21x-ray100CCDBruker DIP-6040HORIZONTAL FOCUSING MIRROR2011-01-22MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9000SPring-8BL44XU
2SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9791, 0.9794, 0.9642SPring-8BL44XU

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
12.730099.90.10318.85.72066654
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)
12.72.81000.3325.72072

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 DIFFRACTIONMADTHROUGHOUT2.7156.271071853999.630.21990.21820.2525RANDOM50.68
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]
3.961.983.96-5.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.063
r_dihedral_angle_4_deg24.327
r_dihedral_angle_3_deg21.14
r_dihedral_angle_1_deg6.865
r_scangle_it3.431
r_scbond_it1.931
r_angle_refined_deg1.785
r_mcangle_it1.163
r_mcbond_it0.564
r_chiral_restr0.111
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.063
r_dihedral_angle_4_deg24.327
r_dihedral_angle_3_deg21.14
r_dihedral_angle_1_deg6.865
r_scangle_it3.431
r_scbond_it1.931
r_angle_refined_deg1.785
r_mcangle_it1.163
r_mcbond_it0.564
r_chiral_restr0.111
r_bond_refined_d0.018
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1827
Nucleic Acid Atoms
Solvent Atoms32
Heterogen Atoms

Software

Software
Software NamePurpose
SCALEPACKdata scaling
SHARPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction