2R61

Crystal structure of the Staphylococcal superantigen-like protein SSL5 in complex with sialyl-Lewis X at pH 7.4


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.429120% PEG 3340, 0.2M disodium tartrate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
3.3162.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.223α = 90
b = 52.223β = 90
c = 236.657γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATEMAR scanner 345 mm platemirrors2006-11-23MSINGLE 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)R Sym 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
12.7559.16499.90.1290.12957.49300
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.752.91000.4840.4841.57.81301

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 1M4V2.7535.07878943999.970.212160.209490.26859RANDOM16.542
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]
-0.01-0.010.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.676
r_dihedral_angle_4_deg25.588
r_dihedral_angle_3_deg19.933
r_dihedral_angle_1_deg7.65
r_scangle_it2.881
r_scbond_it1.852
r_angle_refined_deg1.744
r_mcangle_it1.064
r_mcbond_it0.628
r_nbtor_refined0.329
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.676
r_dihedral_angle_4_deg25.588
r_dihedral_angle_3_deg19.933
r_dihedral_angle_1_deg7.65
r_scangle_it2.881
r_scbond_it1.852
r_angle_refined_deg1.744
r_mcangle_it1.064
r_mcbond_it0.628
r_nbtor_refined0.329
r_nbd_refined0.226
r_symmetry_vdw_refined0.195
r_xyhbond_nbd_refined0.137
r_chiral_restr0.115
r_symmetry_hbond_refined0.107
r_bond_refined_d0.017
r_gen_planes_refined0.005
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_refined
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 Atoms1629
Nucleic Acid Atoms
Solvent Atoms59
Heterogen Atoms73

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction