4OBI

Crystal structure of a DUF1312 family protein (EF3258) from Enterococcus faecalis V583 at 1.73 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	6	293	30.0000% polyethylene glycol 6000, 0.1M MES pH 6.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 27.259	α = 90
b = 49.16	β = 90
c = 71.776	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)	2013-11-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1		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	1.73	40.559	96.4	0.054	15.25			10218		-3	23.033

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	1.73	1.79	78.1		0.684	1.9

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	MOLECULAR REPLACEMENT	THROUGHOUT	1.734	40.559	10216	485	97	0.1704	0.169	0.1992	RANDOM	29.7179

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]
-2.78			0.33		2.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.707
r_dihedral_angle_4_deg	13.967
r_dihedral_angle_3_deg	9.935
r_dihedral_angle_1_deg	6.134
r_mcangle_it	2.354
r_mcbond_it	1.343
r_mcbond_other	1.334
r_angle_refined_deg	1.091
r_angle_other_deg	0.674
r_chiral_restr	0.069

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.707
r_dihedral_angle_4_deg	13.967
r_dihedral_angle_3_deg	9.935
r_dihedral_angle_1_deg	6.134
r_mcangle_it	2.354
r_mcbond_it	1.343
r_mcbond_other	1.334
r_angle_refined_deg	1.091
r_angle_other_deg	0.674
r_chiral_restr	0.069
r_bond_refined_d	0.006
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	685
Nucleic Acid Atoms
Solvent Atoms	79
Heterogen Atoms	9

Software

Software
Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
XSCALE	data scaling
REFMAC	refinement
XDS	data reduction

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.