2OW7

Golgi alpha-mannosidase II complex with (1R,6S,7R,8S)-1-thioniabicyclo[4.3.0]nonan-7,8-diol 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
2.1542.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.9α = 90
b = 108.58β = 90
c = 137.779γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER SMART 60002007-01-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.5418

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
11.772099.50.060619.87.2110136310089311
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)
11.771.8192.90.4023.143.2

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 REPLACEMENTTHROUGHOUT1hty1.7710.54101010100293150999.590.1620.1620.203RANDOM16.853
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.098
r_dihedral_angle_4_deg18.318
r_dihedral_angle_3_deg13.972
r_dihedral_angle_1_deg6.941
r_scangle_it4.758
r_scbond_it3.204
r_angle_refined_deg2.023
r_mcangle_it1.993
r_mcbond_it1.365
r_symmetry_vdw_refined0.328
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.098
r_dihedral_angle_4_deg18.318
r_dihedral_angle_3_deg13.972
r_dihedral_angle_1_deg6.941
r_scangle_it4.758
r_scbond_it3.204
r_angle_refined_deg2.023
r_mcangle_it1.993
r_mcbond_it1.365
r_symmetry_vdw_refined0.328
r_nbtor_refined0.309
r_nbd_refined0.215
r_xyhbond_nbd_refined0.207
r_chiral_restr0.159
r_symmetry_hbond_refined0.149
r_bond_refined_d0.026
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8190
Nucleic Acid Atoms
Solvent Atoms1115
Heterogen Atoms59

Software

Software
Software NamePurpose
SAINTdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PROTEUM PLUSdata collection
SAINTdata reduction
SADABSdata scaling
CNSphasing