3EJS

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3BUB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7298PEG8000, Tris, pH 7, 2.5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2445.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.343α = 90
b = 110.425β = 90
c = 139.857γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42005-07-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE A10.977CHESSA1

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
11.353099.70.100515.598.28235052234434
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)
11.351.3797.50.3324.524.735147

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 REPLACEMENTTHROUGHOUT3BUB1.3529.54234893231933344998.740.1910.1910.213RANDOM15.785
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]
-0.040.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.234
r_dihedral_angle_4_deg17.978
r_dihedral_angle_3_deg12.484
r_dihedral_angle_1_deg6.072
r_scangle_it3.231
r_scbond_it2.243
r_mcangle_it1.51
r_angle_refined_deg1.507
r_mcbond_it1.047
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.234
r_dihedral_angle_4_deg17.978
r_dihedral_angle_3_deg12.484
r_dihedral_angle_1_deg6.072
r_scangle_it3.231
r_scbond_it2.243
r_mcangle_it1.51
r_angle_refined_deg1.507
r_mcbond_it1.047
r_nbtor_refined0.303
r_symmetry_vdw_refined0.215
r_nbd_refined0.198
r_symmetry_hbond_refined0.142
r_xyhbond_nbd_refined0.127
r_chiral_restr0.102
r_bond_refined_d0.015
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8193
Nucleic Acid Atoms
Solvent Atoms1178
Heterogen Atoms46

Software

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