3NEV

Crystal structure of YagE, a prophage protein from E. coli K12 in complex with KDGal

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	6.5	298	100mM HEPES pH 6.5, 200mM MgCl2, 25% PEG 3350, 50mM PYRUVATE, 50mM GLYCERALDEHYDE, Microbatch, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 141.86	α = 90
b = 155.13	β = 90
c = 55.71	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100				2010-04-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.95374	ESRF	BM14

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	2.19	49.18	99.1	0.125	14.01			63549		-3	28.753

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.19	2.25	92.4		0.444	0.47	5.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	2V8Z	2.19	49.18	63549	3178	100	0.199	0.197	0.237	RANDOM	20.613

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]
-1.72			2.58		-0.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.714
r_dihedral_angle_4_deg	17.645
r_dihedral_angle_3_deg	15.177
r_dihedral_angle_1_deg	6.153
r_scangle_it	4.722
r_scbond_it	3.092
r_angle_refined_deg	1.868
r_mcangle_it	1.582
r_mcbond_it	0.878
r_chiral_restr	0.145

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.714
r_dihedral_angle_4_deg	17.645
r_dihedral_angle_3_deg	15.177
r_dihedral_angle_1_deg	6.153
r_scangle_it	4.722
r_scbond_it	3.092
r_angle_refined_deg	1.868
r_mcangle_it	1.582
r_mcbond_it	0.878
r_chiral_restr	0.145
r_bond_refined_d	0.024
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9024
Nucleic Acid Atoms
Solvent Atoms	490
Heterogen Atoms	76

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.