2R61

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1M4V	PDB ENTRY 1M4V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	291	20% PEG 3340, 0.2M disodium tartrate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.31	62.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.223	α = 90
b = 52.223	β = 90
c = 236.657	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	IMAGE PLATE	MAR scanner 345 mm plate	mirrors	2006-11-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.75	59.164	99.9	0.129	0.129	5	7.4		9300

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)	Redundancy	Number Unique Reflections (All)
1	2.75	2.9	100		0.484	0.484	1.5	7.8	1301

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1M4V	2.75	35.07	8789	439	99.97	0.21216	0.20949	0.26859	RANDOM	16.542

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			-0.01		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.676
r_dihedral_angle_4_deg	25.588
r_dihedral_angle_3_deg	19.933
r_dihedral_angle_1_deg	7.65
r_scangle_it	2.881
r_scbond_it	1.852
r_angle_refined_deg	1.744
r_mcangle_it	1.064
r_mcbond_it	0.628
r_nbtor_refined	0.329
r_nbd_refined	0.226
r_symmetry_vdw_refined	0.195
r_xyhbond_nbd_refined	0.137
r_chiral_restr	0.115
r_symmetry_hbond_refined	0.107
r_bond_refined_d	0.017
r_gen_planes_refined	0.005
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 Atoms	Number
Protein Atoms	1629
Nucleic Acid Atoms
Solvent Atoms	59
Heterogen Atoms	73

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction