2YA2 | pdb_00002ya2

Catalytic Module of the Multi-modular glycogen-degrading pneumococcal virulence factor SpuA in complex with an inhibitor.


X-RAY DIFFRACTION

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.3948.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.779α = 90
b = 75.803β = 97.72
c = 88.089γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATERIGAKU R-AXIS IVMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-002

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
12.3720900.085.82.2256382
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)
12.372.4891.10.252.62.14

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.372025638135987.880.210970.208310.20840.259510.2574RANDOM26.407
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]
-0.37-0.440.63-0.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.084
r_dihedral_angle_4_deg18.561
r_dihedral_angle_3_deg16.666
r_dihedral_angle_1_deg6.547
r_scangle_it2.903
r_scbond_it1.853
r_angle_refined_deg1.44
r_mcangle_it1.129
r_mcbond_it0.612
r_chiral_restr0.098
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5636
Nucleic Acid Atoms
Solvent Atoms206
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
SCALAdata scaling