3D51

GOLGI MANNOSIDASE II complex with 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
2.1642.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.739α = 90
b = 109.118β = 90
c = 137.694γ = 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
11.434098.80.07715.56.8191100188859
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)
1.431.4683.50.252.91.67732

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 REPLACEMENTTHROUGHOUT1.4340190972184097273296.40.1870.1870.201RANDOM16.849
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]
-0.480.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.412
r_dihedral_angle_4_deg17.62
r_dihedral_angle_3_deg11.841
r_dihedral_angle_1_deg6.035
r_scangle_it3.824
r_scbond_it2.463
r_mcangle_it1.702
r_angle_refined_deg1.53
r_mcbond_it0.958
r_symmetry_hbond_refined0.584
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.412
r_dihedral_angle_4_deg17.62
r_dihedral_angle_3_deg11.841
r_dihedral_angle_1_deg6.035
r_scangle_it3.824
r_scbond_it2.463
r_mcangle_it1.702
r_angle_refined_deg1.53
r_mcbond_it0.958
r_symmetry_hbond_refined0.584
r_nbtor_refined0.316
r_symmetry_vdw_refined0.22
r_nbd_refined0.207
r_xyhbond_nbd_refined0.133
r_chiral_restr0.102
r_bond_refined_d0.013
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8259
Nucleic Acid Atoms
Solvent Atoms1127
Heterogen Atoms22

Software

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