4RGT | pdb_00004rgt

2.0 Angstrom Crystal Structure of Superantigen-like Protein from Staphylococcus aureus in Complex with 3-N-Acetylneuraminyl-N-acetyllactosamine.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3V05

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	295	Protein: 7.4mG/mL, 0.25M Sodium chloride, 0.01M Tris-HCl (pH 8.3); Screen: Classics II (D3), 0.1M HEPES (pH 7.0), 30% (v/v) Jeffamine ED-2001., VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 141.832	α = 90
b = 141.832	β = 90
c = 41.991	γ = 120

Symmetry
Space Group	P 64

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 225 mm CCD	Beryllium lenses	2014-08-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	30	100	0.063	0.063	25.8	6	32916	32916		-3	35.7

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	2.03	100		0.627	0.627	2.8	6	1606

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	3V05	2	29.31	31234	31234	1669	99.78	0.20028	0.20028	0.19786	0.2	0.24704	0.25	RANDOM	48.964

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]
0.38	0.38		0.38		-1.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.934
r_dihedral_angle_4_deg	14.758
r_dihedral_angle_3_deg	10.943
r_long_range_B_refined	8.378
r_long_range_B_other	8.33
r_scangle_other	3.617
r_dihedral_angle_1_deg	3.535
r_mcangle_it	2.49
r_mcangle_other	2.489
r_scbond_it	2.37
r_scbond_other	2.36
r_mcbond_it	1.709
r_mcbond_other	1.709
r_angle_refined_deg	1.606
r_angle_other_deg	0.708
r_chiral_restr	0.097
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3180
Nucleic Acid Atoms
Solvent Atoms	247
Heterogen Atoms	99

Software

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