3N2X

Crystal structure of YagE, a prophage protein belonging to the dihydrodipicolinic acid synthase family from E. coli K12 in complex with pyruvate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2V8Z

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 141.13	α = 90
b = 153.55	β = 90
c = 55.53	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					M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.973	ESRF	BM14

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.2	48.975	99.3	0.102	0.11	16.93			62107		-3	22.397

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)
	2.2	2.25	96		0.339	0.37	5.9

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	2.2	48.975	62107	3106	100	0.181	0.179	0.222	RANDOM	13.778

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]
-1.32			0.67		0.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.501
r_dihedral_angle_4_deg	19.002
r_dihedral_angle_3_deg	15.223
r_dihedral_angle_1_deg	6.064
r_scangle_it	3.906
r_scbond_it	2.53
r_angle_refined_deg	1.866
r_mcangle_it	1.375
r_mcbond_it	0.772
r_chiral_restr	0.189

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.501
r_dihedral_angle_4_deg	19.002
r_dihedral_angle_3_deg	15.223
r_dihedral_angle_1_deg	6.064
r_scangle_it	3.906
r_scbond_it	2.53
r_angle_refined_deg	1.866
r_mcangle_it	1.375
r_mcbond_it	0.772
r_chiral_restr	0.189
r_bond_refined_d	0.023
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9055
Nucleic Acid Atoms
Solvent Atoms	495
Heterogen Atoms	16

Software

Software
Software Name	Purpose
XSCALE	data scaling
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 R01GM157729.