3EJR

Golgi alpha-Mannosidase II in complex with 5-substitued swainsonine analog: (5R)-5-[2'-oxo-2'-(4-tert-butylphenyl)ethyl]-swainsonine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7298PEG8000, Tris, pH 7, 2.5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthew coefficientSolvent content
2.2144.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.075α = 90
b = 110.023β = 90
c = 139.057γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42004-08-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE F10.9186CHESSF1

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
11.273095.90.08317.45.8278149266666
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)
11.271.373.10.265.12.912623

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3BUB1.2729.36277995262677598594.490.1480.1480.173RANDOM13.197
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.836
r_dihedral_angle_4_deg18.906
r_dihedral_angle_3_deg11.745
r_dihedral_angle_1_deg6.063
r_sphericity_free4.799
r_sphericity_bonded3.746
r_scangle_it3.329
r_scbond_it2.435
r_mcangle_it1.761
r_rigid_bond_restr1.639
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.836
r_dihedral_angle_4_deg18.906
r_dihedral_angle_3_deg11.745
r_dihedral_angle_1_deg6.063
r_sphericity_free4.799
r_sphericity_bonded3.746
r_scangle_it3.329
r_scbond_it2.435
r_mcangle_it1.761
r_rigid_bond_restr1.639
r_angle_refined_deg1.348
r_mcbond_it1.203
r_nbtor_refined0.308
r_nbd_refined0.195
r_symmetry_vdw_refined0.194
r_symmetry_hbond_refined0.136
r_xyhbond_nbd_refined0.116
r_chiral_restr0.09
r_bond_refined_d0.01
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8196
Nucleic Acid Atoms
Solvent Atoms1364
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
SADABSdata scaling
CNSphasing