3DX1

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


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
2.1943.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.917α = 90
b = 109.539β = 90
c = 138.689γ = 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
11.212096.20.06614.16.9305324
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)
11.211.2487.90.543.4418434

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 REPLACEMENTFREE RPDB entry 1HTY1.2120300722258803453094.70.1270.1270.163RANDOM20.368
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
s_approx_iso_adps0.101
s_non_zero_chiral_vol0.091
s_zero_chiral_vol0.078
s_similar_adp_cmpnt0.053
s_angle_d0.031
s_from_restr_planes0.029
s_anti_bump_dis_restr0.023
s_bond_d0.014
s_rigid_bond_adp_cmpnt0.006
s_similar_dist
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8195
Nucleic Acid Atoms
Solvent Atoms1432
Heterogen Atoms37

Software

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