3DX4

Golgi alpha-Mannosidase II in complex with Mannostatin analog (1R,2R,3R,4S,5R)-4-amino-5-methoxycyclopentane-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
2.1843.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.769α = 90
b = 109.703β = 90
c = 138.306γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42007-04-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE A10.9770CHESSA1

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
11.384099.60.07824.214.6212071
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)
11.381.482.80.415.26.72887

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 1HTY1.3819.5212538211539313699.530.1880.1880.203RANDOM15.957
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_deg37.492
r_dihedral_angle_4_deg17.371
r_dihedral_angle_3_deg11.731
r_dihedral_angle_1_deg6.075
r_scangle_it3.554
r_scbond_it2.337
r_mcangle_it1.632
r_angle_refined_deg1.593
r_mcbond_it1.07
r_nbtor_refined0.316
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.492
r_dihedral_angle_4_deg17.371
r_dihedral_angle_3_deg11.731
r_dihedral_angle_1_deg6.075
r_scangle_it3.554
r_scbond_it2.337
r_mcangle_it1.632
r_angle_refined_deg1.593
r_mcbond_it1.07
r_nbtor_refined0.316
r_symmetry_vdw_refined0.258
r_nbd_refined0.231
r_chiral_restr0.157
r_symmetry_hbond_refined0.151
r_xyhbond_nbd_refined0.137
r_bond_refined_d0.014
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8197
Nucleic Acid Atoms
Solvent Atoms1304
Heterogen Atoms34

Software

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