2RDG

Crystal structure of Staphylococcal Superantigen-Like protein 11 in complex with Sialyl Lewis X


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1M4VPDB ENTRY 1M4V

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29120% PEG3350, 0.2M potassium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.6453.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.031α = 90
b = 57.945β = 101.83
c = 43.462γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113IMAGE PLATERIGAKU RAXIS IVMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
11.630.791.50.0547.228611
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)
11.61.6980.10.11410.17.13623

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1M4V1.622.4528588143091.630.175760.174170.20656RANDOM23.827
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]
-0.01-0.03-0.030.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.395
r_dihedral_angle_4_deg13.582
r_dihedral_angle_3_deg11.122
r_dihedral_angle_1_deg5.904
r_scangle_it2.726
r_scbond_it1.734
r_angle_refined_deg1.21
r_mcangle_it1.003
r_mcbond_it0.549
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.395
r_dihedral_angle_4_deg13.582
r_dihedral_angle_3_deg11.122
r_dihedral_angle_1_deg5.904
r_scangle_it2.726
r_scbond_it1.734
r_angle_refined_deg1.21
r_mcangle_it1.003
r_mcbond_it0.549
r_nbtor_refined0.306
r_nbd_refined0.202
r_symmetry_hbond_refined0.192
r_symmetry_vdw_refined0.152
r_xyhbond_nbd_refined0.115
r_chiral_restr0.084
r_metal_ion_refined0.083
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1553
Nucleic Acid Atoms
Solvent Atoms350
Heterogen Atoms72

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing