2Z8L

Crystal Structure of the Staphylococcal superantigen-like protein SSL5 at pH 4.6 complexed 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 DROP4.629120% PEG 3350, 0.2M NaH2PO4, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.6553.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.625α = 90
b = 78.237β = 127.02
c = 55.276γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARMOSAIC 325 mm CCDmirror, monochromator2006-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.97892SSRLBL9-2

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
11.6530.0499.80.05125.67.43072830702
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)
11.651.741000.6672.57.44497

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1M4V1.6528.053079030702153899.810.1830.1830.1810.218RANDOM16.92
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]
0.310.37-0.220.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.736
r_dihedral_angle_4_deg15.319
r_dihedral_angle_3_deg13.459
r_dihedral_angle_1_deg6.175
r_scangle_it4.532
r_scbond_it3.517
r_mcangle_it2.093
r_mcbond_it1.866
r_angle_refined_deg1.744
r_angle_other_deg0.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.736
r_dihedral_angle_4_deg15.319
r_dihedral_angle_3_deg13.459
r_dihedral_angle_1_deg6.175
r_scangle_it4.532
r_scbond_it3.517
r_mcangle_it2.093
r_mcbond_it1.866
r_angle_refined_deg1.744
r_angle_other_deg0.91
r_mcbond_other0.358
r_symmetry_vdw_other0.236
r_nbd_refined0.21
r_nbd_other0.194
r_nbtor_refined0.188
r_symmetry_vdw_refined0.166
r_xyhbond_nbd_refined0.153
r_symmetry_hbond_refined0.143
r_chiral_restr0.115
r_nbtor_other0.094
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1607
Nucleic Acid Atoms
Solvent Atoms111
Heterogen Atoms67

Software

Software
Software NamePurpose
MOSFLMdata reduction
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
SCALAdata scaling