2HTH

Structural basis for ubiquitin recognition by the human EAP45/ESCRT-II GLUE domain


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529810% PEG8000; 10% Ethylene glycol; 100mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.9157.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.727α = 90
b = 102.727β = 90
c = 54.306γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2006-02-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.10000, 0.97910NSLSX29A

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
12.75097.70.109118264
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)
2.72.881.40.536

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 DIFFRACTIONSADTHROUGHOUT2.737.32742681097.730.251840.247750.28872RANDOM56.345
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]
-1.73-1.733.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.972
r_dihedral_angle_3_deg15.795
r_dihedral_angle_4_deg14
r_dihedral_angle_1_deg7.251
r_scangle_it3.68
r_scbond_it2.333
r_mcangle_it1.814
r_angle_refined_deg1.681
r_mcbond_it1.032
r_nbtor_refined0.317
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.972
r_dihedral_angle_3_deg15.795
r_dihedral_angle_4_deg14
r_dihedral_angle_1_deg7.251
r_scangle_it3.68
r_scbond_it2.333
r_mcangle_it1.814
r_angle_refined_deg1.681
r_mcbond_it1.032
r_nbtor_refined0.317
r_nbd_refined0.201
r_symmetry_vdw_refined0.199
r_xyhbond_nbd_refined0.148
r_chiral_restr0.107
r_bond_refined_d0.018
r_gen_planes_refined0.005
r_bond_other_d
r_metal_ion_refined
r_metal_ion_other
r_sphericity_bonded
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_nbd_other
r_mcbond_other
r_angle_other_deg
r_nbtor_other
r_gen_planes_other
r_rigid_bond_restr
r_sphericity_free
r_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1640
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction