5DKY

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72931.2 M sodium citrate tribasic, 0.1 M Tris-HCl (pH 7.0), 2.5 mM DNJ
Crystal Properties
Matthews coefficientSolvent content
2.5151.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 189.523α = 90
b = 189.523β = 90
c = 157.784γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 2702013-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NE3A0.97946Photon FactoryAR-NE3A

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
11.65098.30.08623.62.8141836-3
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)
11.61.63980.4192.82.6

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 DIFFRACTIONSADTHROUGHOUT1.620133918709299.420.1560.1550.184RANDOM20.444
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]
-0.05-0.03-0.050.16
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined4.551
r_long_range_B_other4.234
r_scangle_other3.059
r_scbond_it1.934
r_scbond_other1.934
r_mcangle_it1.901
r_mcangle_other1.901
r_angle_refined_deg1.427
r_mcbond_it1.255
r_mcbond_other1.253
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined4.551
r_long_range_B_other4.234
r_scangle_other3.059
r_scbond_it1.934
r_scbond_other1.934
r_mcangle_it1.901
r_mcangle_other1.901
r_angle_refined_deg1.427
r_mcbond_it1.255
r_mcbond_other1.253
r_angle_other_deg0.795
r_chiral_restr0.087
r_bond_refined_d0.011
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 Atoms7485
Nucleic Acid Atoms
Solvent Atoms819
Heterogen Atoms11

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing