5NKZ

Crystal structure of H. polymorpha ubiquitin conjugating enzyme Pex4p in complex with soluble domain of Pex22p


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52930.1 M BIS-TRIS Propane pH 7.8, 0.2 M sodium sulphate, 22 % w/v PEG-3350
Crystal Properties
Matthews coefficientSolvent content
2.8256.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.683α = 89.18
b = 61.582β = 78.02
c = 78.441γ = 84.09
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-07-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, DESY BEAMLINE P110.98PETRA III, DESYP11

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
12.8548.039795.020.1236.033.9320450
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)
12.852.9594.50.81.145.49

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPex4:Pex22 complex coordinates from S. cerevisae (PDB: 2Y9M(Williams et al. 2012); 33/57 % and 14/35 % identity/similarity, respectively) as starting model2.8548.03971845198095.020.23850.236080.2837RANDOM74.337
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]
2.85-0.04-2.49-0.815.69-3.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.019
r_dihedral_angle_4_deg23.592
r_dihedral_angle_3_deg20.173
r_dihedral_angle_1_deg8.281
r_long_range_B_refined6.058
r_long_range_B_other6.058
r_mcangle_it3.826
r_mcangle_other3.825
r_scangle_other3.657
r_mcbond_it2.327
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.019
r_dihedral_angle_4_deg23.592
r_dihedral_angle_3_deg20.173
r_dihedral_angle_1_deg8.281
r_long_range_B_refined6.058
r_long_range_B_other6.058
r_mcangle_it3.826
r_mcangle_other3.825
r_scangle_other3.657
r_mcbond_it2.327
r_mcbond_other2.326
r_scbond_it2.141
r_scbond_other2.14
r_angle_refined_deg1.925
r_angle_other_deg1.158
r_chiral_restr0.119
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4639
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
MOLREPphasing
Aimlessdata scaling