4NW4 | pdb_00004nw4

Crystal structure of a DUF4822 family protein (EF0375) from Enterococcus faecalis V583 at 1.85 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	277	2.400M ammonium sulfate, 0.1M TRIS pH 8.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.379	α = 90
b = 61.379	β = 90
c = 160.389	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)	2013-02-21	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 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	26.731	99.9	0.136	9.4	6.6	29118	29118

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	1.9	99.9		0.013	1.264	0.6	6.9	2140

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.85	26.731	29054	1477	99.86	0.1512	0.1496	0.16	0.1815	0.19	RANDOM	29.0028

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]
0.72	0.72		0.72		-2.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.464
r_dihedral_angle_4_deg	12.74
r_dihedral_angle_3_deg	11.043
r_dihedral_angle_1_deg	6.753
r_mcangle_it	2.864
r_mcbond_it	2.34
r_mcbond_other	2.338
r_angle_refined_deg	1.384
r_angle_other_deg	0.716
r_chiral_restr	0.086

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.464
r_dihedral_angle_4_deg	12.74
r_dihedral_angle_3_deg	11.043
r_dihedral_angle_1_deg	6.753
r_mcangle_it	2.864
r_mcbond_it	2.34
r_mcbond_other	2.338
r_angle_refined_deg	1.384
r_angle_other_deg	0.716
r_chiral_restr	0.086
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2150
Nucleic Acid Atoms
Solvent Atoms	270
Heterogen Atoms	57

Software

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

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 R01GM157729.