7P5R

Racemic protein crystal structure of lacticin Q from Lactococcus lactis

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	A racemic mixture of L-lacticin Q and D-lacticin Q at 27 mg/mL concentration was mixed 1:1 with 4.0M sodium formate precipitant condition pH 7.0 in a 1 microlitre sitting drop. Crystals were submerged in 2.0M Lithium sulfate cryoprotectant and flash frozen in liquid nitrogen during harvesting.

Crystal Properties
Matthews coefficient	Solvent content
1.81	31.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 24.21	α = 95.03
b = 27.83	β = 90.43
c = 70.45	γ = 115.41

Symmetry
Space Group	P 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		2020-09-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.8156	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	0.96	35.05	93	0.999	11.3	3.5		93924

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	0.96	0.98	84.2		0.67	1

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	Ideal helix fragments	0.96	35.05	93922	4686	92.978	0.183	0.1823	0.2053	13.581

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]
-0.28	0.374	-0.818	-0.053	-0.852	0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	51.702
r_dihedral_angle_3_deg	13.061
r_rigid_bond_restr	5.436
r_dihedral_angle_1_deg	3.923
r_lrange_it	2.616
r_lrange_other	2.546
r_scangle_it	2.54
r_scangle_other	2.54
r_scbond_it	2.255
r_scbond_other	2.252
r_angle_refined_deg	1.817
r_mcangle_other	1.733
r_mcangle_it	1.732
r_mcbond_other	1.357
r_mcbond_it	1.356
r_angle_other_deg	1.319
r_nbd_other	0.35
r_symmetry_nbd_refined	0.312
r_nbd_refined	0.244
r_symmetry_xyhbond_nbd_refined	0.235
r_symmetry_nbd_other	0.207
r_nbtor_refined	0.199
r_xyhbond_nbd_refined	0.168
r_chiral_restr	0.102
r_symmetry_nbtor_other	0.073
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.008
r_gen_planes_other	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1672
Nucleic Acid Atoms
Solvent Atoms	189
Heterogen Atoms	21

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
Fragon	phasing
Coot	model building
SHELXE	model building
XDS	data reduction
xia2	data reduction