4EF2

Crystal structure of a pheromone cOB1 precursor/lipoprotein, YaeC family (EF2496) from Enterococcus faecalis V583 at 2.10 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9.5	293	30.0% polyethylene glycol 400, 0.1M CHES pH 9.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.225	α = 90
b = 75.691	β = 90
c = 143.815	γ = 90

Symmetry
Space Group	P 21 21 21

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	Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)	2012-02-08	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97966,0.97901	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.1	28.763	90.6	0.04	12.37			28845		-3	38.876

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.17	64.9		0.746	1.4

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	MAD	THROUGHOUT	2.1	28.763	28794	1458	95.25	0.1898	0.1875	0.2322	RANDOM	52.5789

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]
-3.82			-0.87		4.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.808
r_dihedral_angle_4_deg	14.003
r_dihedral_angle_3_deg	12.346
r_dihedral_angle_1_deg	5.359
r_angle_refined_deg	1.858
r_angle_other_deg	1.465
r_nbd_other	0.215
r_nbd_refined	0.214
r_nbtor_refined	0.171
r_symmetry_vdw_other	0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.808
r_dihedral_angle_4_deg	14.003
r_dihedral_angle_3_deg	12.346
r_dihedral_angle_1_deg	5.359
r_angle_refined_deg	1.858
r_angle_other_deg	1.465
r_nbd_other	0.215
r_nbd_refined	0.214
r_nbtor_refined	0.171
r_symmetry_vdw_other	0.14
r_symmetry_vdw_refined	0.122
r_nbtor_other	0.108
r_chiral_restr	0.105
r_bond_refined_d	0.017
r_gen_planes_refined	0.009
r_bond_other_d	0.006
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3746
Nucleic Acid Atoms
Solvent Atoms	98
Heterogen Atoms	68

Software

Software
Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
REFMAC	refinement
XDS	data reduction
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.