4KH8

Crystal structure of a Lipocalin-like protein (EF0376) from Enterococcus faecalis V583 at 1.60 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	12.0% Glycerol, 1.5M ammonium sulfate, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.745	α = 90
b = 99.745	β = 90
c = 56.956	γ = 120

Symmetry
Space Group	P 65

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)	2013-03-22	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97903,0.97871	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.6	27.046	99.9	0.121	10.5	6.2	42670	42670

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	1.6	1.64	100		0.681	0.681	1.1	6.4	3160

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	1.6	27.046	42647	2150	99.84	0.1424	0.1408	0.1727	RANDOM	16.6849

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]
-0.03	-0.03		-0.03		0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.267
r_dihedral_angle_4_deg	15.769
r_dihedral_angle_3_deg	10.508
r_dihedral_angle_1_deg	6.648
r_mcangle_it	2.287
r_mcbond_it	1.563
r_mcbond_other	1.563
r_angle_refined_deg	1.533
r_angle_other_deg	0.783
r_chiral_restr	0.095

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.267
r_dihedral_angle_4_deg	15.769
r_dihedral_angle_3_deg	10.508
r_dihedral_angle_1_deg	6.648
r_mcangle_it	2.287
r_mcbond_it	1.563
r_mcbond_other	1.563
r_angle_refined_deg	1.533
r_angle_other_deg	0.783
r_chiral_restr	0.095
r_bond_refined_d	0.014
r_gen_planes_refined	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	2501
Nucleic Acid Atoms
Solvent Atoms	351
Heterogen Atoms	40

Software

Software
Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
SCALA	data scaling
REFMAC	refinement
MOSFLM	data reduction
SHELXD	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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.