8AVT | pdb_00008avt

Racemic protein crystal structure of aureocin A53 from Staphylococcus aureus in the presence of glycerol 3-phosphate

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	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 acetate, 0.2 M sodium citrate and 29% PEG 4000 v/v precipitant condition, pH 5.6 in a 1 microlitre sitting drop. The crystal was soaked with sn-glycerol-3-phosphate (334 mM in the precipitant solution) at 1:1 v/v for 24 hours (50 equivalents). 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
3.26	62.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.718	α = 90
b = 37.239	β = 92.973
c = 114.088	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	1.2	34.531	99.9	0.999	8.2	13.4		96953

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	1.2	1.22	99.6		0.88	1.3	13.6

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	1.2	34.531	96947	4912	99.866	0.177	0.176	0.18	0.2033	0.21	19.865

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]
-0.065		0.108	0.923		-0.864

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.925
r_dihedral_angle_3_deg	13.01
r_dihedral_angle_1_deg	4.816
r_lrange_it	3.326
r_lrange_other	3.053
r_scangle_it	3.032
r_scangle_other	3.031
r_rigid_bond_restr	2.818
r_scbond_it	2.717
r_scbond_other	2.626
r_mcangle_it	1.75
r_mcangle_other	1.749
r_angle_refined_deg	1.703
r_mcbond_other	1.638
r_mcbond_it	1.637
r_angle_other_deg	1.188
r_nbd_other	0.38
r_symmetry_nbd_refined	0.247
r_nbd_refined	0.239
r_nbtor_refined	0.203
r_symmetry_nbd_other	0.188
r_xyhbond_nbd_refined	0.172
r_symmetry_xyhbond_nbd_refined	0.161
r_symmetry_xyhbond_nbd_other	0.134
r_chiral_restr	0.103
r_symmetry_nbtor_other	0.076
r_xyhbond_nbd_other	0.026
r_bond_refined_d	0.011
r_gen_planes_refined	0.011
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	396
Heterogen Atoms	53

Software

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