8AVR | pdb_00008avr

Racemic protein crystal structure of aureocin A53 from Staphylococcus aureus in the presence of sulfate

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	292	A racemic mixture of L-Aureocin A53 and D-Aureocin A53 at 40 mg/mL concentration was mixed 1:1 with 0.2 M ammonium sulphate, 0.1 M sodium acetate and 24.5% PEG 4000 v/v precipitant condition, pH 5.6 in a 1 microlitre sitting drop. Crystals were submerged in 20% PEG 400 in the precipitant solution as cryoprotectant and flash frozen in liquid nitrogen during harvesting.

Crystal Properties
Matthews coefficient	Solvent content
2.93	58.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.74	α = 90
b = 36.58	β = 95.98
c = 106.15	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 PILATUS 6M-F		2019-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9119	Diamond	I04-1

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	1.13	36.2	86	0.995	9.7	3		89417

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	1.13	1.15	38.7		0.787	1.4	1.2

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2N8O	1.13	36.198	89417	4466	85.703	0.184	0.1825	0.19	0.209	0.21	14.71

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]
0.141		0.619	-0.495		0.219

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.892
r_dihedral_angle_3_deg	13.431
r_dihedral_angle_1_deg	4.945
r_lrange_other	2.339
r_lrange_it	2.338
r_scangle_it	1.787
r_scangle_other	1.77
r_scbond_it	1.442
r_scbond_other	1.432
r_angle_refined_deg	1.404
r_mcangle_it	1.158
r_mcangle_other	1.157
r_angle_other_deg	1.128
r_rigid_bond_restr	1.028
r_mcbond_it	0.895
r_mcbond_other	0.894
r_nbd_other	0.304
r_symmetry_nbd_refined	0.273
r_nbd_refined	0.226
r_nbtor_refined	0.211
r_symmetry_nbd_other	0.17
r_symmetry_xyhbond_nbd_refined	0.143
r_xyhbond_nbd_refined	0.137
r_chiral_restr	0.08
r_symmetry_nbtor_other	0.073
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_symmetry_xyhbond_nbd_other	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1704
Nucleic Acid Atoms
Solvent Atoms	417
Heterogen Atoms	50

Software

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