2OW6

Golgi alpha-mannosidase II complex with (1r,5s,6s,7r,8s)-1-thioniabicyclo[4.3.0]nonan-5,7,8-triol chloride


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HTY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7298Tris, PEG 6K, MPD, NaCl, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.9445.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.007α = 90
b = 109.62β = 90
c = 138.915γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42006-06-01MSINGLE 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
11.193099.10.0859.67.433063111
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)
11.191.2294.10.6411.93.622202

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)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 REPLACEMENTFREE R1HTY1.19303336342325509325509500597.50.1180.1180.1503RANDOM
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]
Coordinate Error
Structure Solution MethodRefinement High ResolutionRefinement Low Resolution
386945.319708
RMS Deviations
KeyRefinement Restraint Deviation
s_anti_bump_dis_restr0.211
s_approx_iso_adps0.11
s_zero_chiral_vol0.083
s_non_zero_chiral_vol0.08
s_similar_adp_cmpnt0.054
s_angle_d0.03
s_from_restr_planes0.0294
s_bond_d0.014
s_rigid_bond_adp_cmpnt0.005
s_similar_dist
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8193
Nucleic Acid Atoms
Solvent Atoms1462
Heterogen Atoms45

Software

Software
Software NamePurpose
SHELXL-97refinement
CNSrefinement
ADSCdata collection
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing