4DN1

Crystal structure of an ENOLASE (mandelate racemase subgroup member) from Agrobacterium tumefaciens (target EFI-502088) with bound mg and formate

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	sitting drop vapor diffuction	4.6	298	Protein (10 mM Tris pH 8.0, 150 mM NaCl, 5 mM MgCl2, 1 mM D,L-glycerate; Reservoir (0.1 M NaAcetate pH 4.6, 3.5 M NaFormate); Cryoprotection (Reservoir, 50 mM MgCl2, 20% Glycerol), sitting drop vapor diffuction, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.14	60.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.36	α = 90
b = 102.36	β = 90
c = 369.62	γ = 120

Symmetry
Space Group	P 65 2 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	CCD	RAYONIX MX225HE	MIRRORS	2011-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.9793	APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.05	50	100	0.108	0.108	15.8	11.7		72945			27.5

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	2.05	2.16	100		0.517	0.517	4.5	10.8	10419

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	2NQL	2.05	41.706	1.34	72945	72945	3677	99.98	0.1631	0.1631	0.1614	0.1935	RANDOM	29.1014

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]
0.7921			0.7921		-1.5842

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.245
f_angle_d	1.053
f_chiral_restr	0.073
f_bond_d	0.008
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5978
Nucleic Acid Atoms
Solvent Atoms	656
Heterogen Atoms	6

Software

Software
Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
PHENIX	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.