3I48

Crystal structure of beta toxin from Staphylococcus aureus F277A, P278A mutant with bound magnesium ions

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	PEG 4000, 0.1 M MES, 5mM MgCl2, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
1.89	34.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.9	α = 90
b = 68.577	β = 90
c = 126.559	γ = 90

Symmetry
Space Group	P 21 21 21

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	ADSC QUANTUM 315	mirrors	2007-10-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.90020	APS	14-BM-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.8	50	99.8	0.055	11.7	4.3	51464	51464

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)
	1.8	1.83	99.5		0.472	2.6	3.8	2493

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3I41	1.8	28.16	51405	48742	2625	99.84	0.185	0.184	0.22	RANDOM	28.979

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]
0.06			-0.13		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.67
r_dihedral_angle_3_deg	15.135
r_dihedral_angle_4_deg	9.516
r_dihedral_angle_1_deg	6.914
r_scangle_it	3.532
r_scbond_it	2.367
r_mcangle_it	1.87
r_angle_refined_deg	1.471
r_mcbond_it	1.116
r_nbtor_refined	0.313

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.67
r_dihedral_angle_3_deg	15.135
r_dihedral_angle_4_deg	9.516
r_dihedral_angle_1_deg	6.914
r_scangle_it	3.532
r_scbond_it	2.367
r_mcangle_it	1.87
r_angle_refined_deg	1.471
r_mcbond_it	1.116
r_nbtor_refined	0.313
r_symmetry_vdw_refined	0.279
r_nbd_refined	0.213
r_symmetry_hbond_refined	0.187
r_xyhbond_nbd_refined	0.145
r_chiral_restr	0.129
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4666
Nucleic Acid Atoms
Solvent Atoms	472
Heterogen Atoms	12

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
CrystalClear	data reduction
AMoRE	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.