2YA0 | pdb_00002ya0

Catalytic Module of the Multi-modular glycogen-degrading pneumococcal virulence factor SpuA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FHFPDB ENTRY 2FHF

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.3247.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.574α = 90
b = 75.196β = 97.31
c = 87.038γ = 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
11.852096.70.0610.23.73576972
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)
11.851.9294.10.42.33.64

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2FHF1.852057697308596.690.174520.171770.170.226620.22RANDOM27.763
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]
-0.36-0.30.63-0.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.468
r_dihedral_angle_4_deg19.02
r_dihedral_angle_3_deg14.459
r_dihedral_angle_1_deg6.423
r_scangle_it4.75
r_scbond_it3.139
r_angle_refined_deg1.927
r_mcangle_it1.844
r_mcbond_it1.149
r_chiral_restr0.155
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5678
Nucleic Acid Atoms
Solvent Atoms838
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
SCALAdata scaling