3DX3

Golgi alpha-Mannosidase II in complex with Mannostatin analog (1R,2R,3S,4R,5R)-5-aminocyclopentane-1,2,3,4-tetraol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HTYPDB entry 1hty

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7298PEG8000, Tris, 2.5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7
Crystal Properties
Matthews coefficientSolvent content
2.244.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.062α = 90
b = 109.977β = 90
c = 138.66γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42007-04-20MSINGLE 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
11.424097.10.07418.27.4193233
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)
11.421.4678.80.266.65.111985

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 REPLACEMENTTHROUGHOUTPDB entry 1hty1.4219.52198768192268286796.730.1490.1480.174RANDOM14.421
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_deg37.141
r_dihedral_angle_4_deg16.963
r_dihedral_angle_3_deg12.184
r_dihedral_angle_1_deg6.068
r_sphericity_free4.78
r_scangle_it3.998
r_sphericity_bonded3.078
r_scbond_it2.743
r_mcangle_it2.001
r_rigid_bond_restr1.597
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.141
r_dihedral_angle_4_deg16.963
r_dihedral_angle_3_deg12.184
r_dihedral_angle_1_deg6.068
r_sphericity_free4.78
r_scangle_it3.998
r_sphericity_bonded3.078
r_scbond_it2.743
r_mcangle_it2.001
r_rigid_bond_restr1.597
r_angle_refined_deg1.47
r_mcbond_it1.384
r_nbtor_refined0.314
r_symmetry_vdw_refined0.257
r_nbd_refined0.202
r_symmetry_hbond_refined0.158
r_chiral_restr0.156
r_xyhbond_nbd_refined0.131
r_bond_refined_d0.011
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8187
Nucleic Acid Atoms
Solvent Atoms1399
Heterogen Atoms38

Software

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