2WYI

Structure of the Streptococcus pyogenes family GH38 alpha-mannosidase complexed with swainsonine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WYHPDB ENTRY 2WYH

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1715 MG/ML 3C CLEAVED SPGH38 MIXED WITH 3% V/V GLYCEROL, 54% V/V TACSIMATE (PH 7.0) AND 2% V/V POLYETHYLENE GLYCOL 6000
Crystal Properties
Matthews coefficientSolvent content
3.8469

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 178.68α = 90
b = 178.68β = 90
c = 198.237γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2008-11-21MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
12.65099.80.0527.76.8931812
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)
12.62.691000.394.17

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMADTHROUGHOUTPDB ENTRY 2WYH2.6132.4593181488899.70.1890.1870.223RANDOM28.09
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]
0.890.89-1.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.958
r_dihedral_angle_4_deg19.023
r_dihedral_angle_3_deg14.68
r_dihedral_angle_1_deg5.724
r_scangle_it2.041
r_scbond_it1.193
r_angle_refined_deg1.111
r_mcangle_it0.782
r_mcbond_it0.396
r_chiral_restr0.075
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.958
r_dihedral_angle_4_deg19.023
r_dihedral_angle_3_deg14.68
r_dihedral_angle_1_deg5.724
r_scangle_it2.041
r_scbond_it1.193
r_angle_refined_deg1.111
r_mcangle_it0.782
r_mcbond_it0.396
r_chiral_restr0.075
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14274
Nucleic Acid Atoms
Solvent Atoms345
Heterogen Atoms114

Software

Software
Software NamePurpose
PHASERmodel building
SCALEPACKdata scaling
SHARPphasing
SHELXphasing
RESOLVEphasing
PHASERphasing
REFMACrefinement