5DL0

Crystal structure of glucosidase II alpha subunit (Glc1Man2-bound from)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82931.2 M sodium citrate tribasic and 0.1 M Tris-HCl (pH 8.0), 5 mM Glc1Man2
Crystal Properties
Matthews coefficientSolvent content
2.5351.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 189.72α = 90
b = 189.72β = 90
c = 158.345γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDRAYONIX MX300HE2014-06-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.90000SPring-8BL44XU

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
12.3501000.10831.67.54869648681-3
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)
12.32.341000.4577.27.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.32045997243099.810.1460.1440.189RANDOM25.866
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]
-0.21-0.11-0.210.69
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined4.73
r_long_range_B_other4.705
r_scangle_other4.09
r_mcangle_other2.783
r_mcangle_it2.782
r_scbond_it2.42
r_scbond_other2.419
r_mcbond_it1.748
r_mcbond_other1.744
r_angle_refined_deg1.453
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined4.73
r_long_range_B_other4.705
r_scangle_other4.09
r_mcangle_other2.783
r_mcangle_it2.782
r_scbond_it2.42
r_scbond_other2.419
r_mcbond_it1.748
r_mcbond_other1.744
r_angle_refined_deg1.453
r_angle_other_deg0.784
r_chiral_restr0.083
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7446
Nucleic Acid Atoms
Solvent Atoms360
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing