8AVU

Racemic protein crystal structure of aureocin A53 from Staphylococcus aureus in the dimeric state

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	292	A racemic mixture of L-Aureocin A53 and D-Aureocin A53 at 40 mg/mL concentration was mixed 1:1 with 0.7 M sodium citrate, 0.1 M Tris precipitant condition, pH 8.5 in a 0.4 microlitre sitting drop. Crystals were submerged in 2.0 M lithium sulphate as cryoprotectant and flash frozen in liquid nitrogen during harvesting.

Crystal Properties
Matthews coefficient	Solvent content
1.84	33.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.56	α = 90
b = 23.077	β = 114.351
c = 52.609	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER2 XE 16M		2020-11-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.8153	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	0.89	21.99	92.7	1	17.2	5.9		62368

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	0.89	0.91	46.4		0.831	1	3.5

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2N8O	0.89	21.99	62367	3106	92.749	0.195	0.1938	0.2105	11.304

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]
-0.34		0.178	-0.317		0.351

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.568
r_dihedral_angle_3_deg	10.752
r_dihedral_angle_1_deg	5.178
r_lrange_it	2.631
r_lrange_other	2.63
r_rigid_bond_restr	1.909
r_scangle_it	1.814
r_scangle_other	1.813
r_angle_refined_deg	1.713
r_scbond_it	1.563
r_scbond_other	1.561
r_mcangle_it	1.203
r_mcangle_other	1.202
r_angle_other_deg	1.168
r_mcbond_it	0.85
r_mcbond_other	0.845
r_nbd_other	0.277
r_symmetry_xyhbond_nbd_refined	0.248
r_xyhbond_nbd_refined	0.247
r_nbd_refined	0.243
r_symmetry_nbd_refined	0.243
r_symmetry_nbd_other	0.214
r_nbtor_refined	0.203
r_symmetry_xyhbond_nbd_other	0.182
r_chiral_restr	0.095
r_symmetry_nbtor_other	0.081
r_gen_planes_refined	0.011
r_bond_refined_d	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	852
Nucleic Acid Atoms
Solvent Atoms	146
Heterogen Atoms	47

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building