3BKX

Crystal structure of cyclopropane-fatty-acyl-phospholipid synthase-like protein (YP_807781.1) from Lactobacillus casei ATCC 334 at 1.85 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	277	NANODROP, 0.2M NH4OAc, 30.0% PEG 4000, 0.1M Citrate pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.136	α = 90
b = 42.381	β = 103.87
c = 154.014	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	CCD	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2007-11-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.97916	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.85	40.825	99.5	0.146	0.146	5.1	5.2		45283			13.78

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.95	97.2		0.611	0.611	1.3	4.6	6400

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	SAD	THROUGHOUT	1.85	40.825	45282	2285	99.41	0.188	0.185	0.242	RANDOM	14.309

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]
0.21		-1	0.64		-1.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.209
r_dihedral_angle_4_deg	16.748
r_dihedral_angle_3_deg	14.089
r_dihedral_angle_1_deg	5.831
r_scangle_it	3.457
r_scbond_it	2.338
r_angle_refined_deg	1.488
r_mcangle_it	1.369
r_angle_other_deg	1.011
r_mcbond_it	0.797

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.209
r_dihedral_angle_4_deg	16.748
r_dihedral_angle_3_deg	14.089
r_dihedral_angle_1_deg	5.831
r_scangle_it	3.457
r_scbond_it	2.338
r_angle_refined_deg	1.488
r_mcangle_it	1.369
r_angle_other_deg	1.011
r_mcbond_it	0.797
r_mcbond_other	0.213
r_chiral_restr	0.089
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4152
Nucleic Acid Atoms
Solvent Atoms	492
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHARP	phasing
SHELXD	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.