5I4D | pdb_00005i4d

1.75 Angstrom Crystal Structure of Superantigen-like Protein, Exotoxin from Staphylococcus aureus, in Complex with Sialyl-LewisX.

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4RCO	PDB-4RCO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.3	292	Protein: 6.1 mg/ml, 0.5M Sodium chloride, 0.01M Tris-HCL (pH 8.3), 2mM Sialyl-LewisX;Screen: JCSG+ (A3), 0.18M tri-Ammonium citrate, 20% (w/v) PEG3350.

Crystal Properties
Matthews coefficient	Solvent content
1.56	21.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.975	α = 90
b = 166.881	β = 90
c = 34.144	γ = 90

Symmetry
Space Group	P 21 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	100	CCD	MARMOSAIC 300 mm CCD	C(111)	2014-10-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	1.75	30	100	0.091	0.091	19.5	7.3		50461		-3	19.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.78	100		0.622	3.1	7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB-4RCO	1.75	29.94	47830	2563	99.62	0.16287	0.16083	0.1702	0.20177	0.2097	RANDOM	22.845

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]
-0.09			0.83		-0.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.751
r_dihedral_angle_4_deg	22.144
r_dihedral_angle_3_deg	10.282
r_long_range_B_refined	6.644
r_long_range_B_other	6.249
r_dihedral_angle_1_deg	3.706
r_scangle_other	2.666
r_mcangle_it	1.676
r_mcangle_other	1.676
r_scbond_it	1.657
r_scbond_other	1.656
r_angle_refined_deg	1.546
r_mcbond_it	1.044
r_mcbond_other	1.043
r_angle_other_deg	0.817
r_chiral_restr	0.098
r_gen_planes_refined	0.022
r_gen_planes_other	0.018
r_bond_refined_d	0.01
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3182
Nucleic Acid Atoms
Solvent Atoms	641
Heterogen Atoms	163

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing