3D52

GOLGI MANNOSIDASE II complex with an N-aryl carbamate derivative of gluco-hydroxyiminolactam


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7298PEG8000, Tris, pH 7, 2.5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1241.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.579α = 90
b = 107.912β = 90
c = 137.062γ = 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
11.62097.40.08713.74.99134545131084
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)
1.61.6396.90.2087.375.34837

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.619.72134349131030194097.530.2290.2280.24RANDOM17.147
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]
0.01-0.040.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.342
r_dihedral_angle_4_deg18.707
r_dihedral_angle_3_deg12.833
r_dihedral_angle_1_deg6.352
r_scangle_it4.384
r_scbond_it2.908
r_mcangle_it1.948
r_angle_refined_deg1.863
r_mcbond_it1.363
r_nbtor_refined0.319
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.342
r_dihedral_angle_4_deg18.707
r_dihedral_angle_3_deg12.833
r_dihedral_angle_1_deg6.352
r_scangle_it4.384
r_scbond_it2.908
r_mcangle_it1.948
r_angle_refined_deg1.863
r_mcbond_it1.363
r_nbtor_refined0.319
r_symmetry_vdw_refined0.311
r_nbd_refined0.217
r_symmetry_hbond_refined0.199
r_xyhbond_nbd_refined0.15
r_chiral_restr0.119
r_bond_refined_d0.017
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8209
Nucleic Acid Atoms
Solvent Atoms875
Heterogen Atoms44

Software

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