4H19

Crystal structure of an enolase (mandelate racemase subgroup, target EFI-502087) from agrobacterium tumefaciens, with bound Mg and d-ribonohydroxamate, ordered loop

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3TJ4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	sitting drop vapor diffuction	4	298	Protein (10 mM Tris, pH 8.0, 200 mM NaCl, 5 mM Mg, 10 mM D-ribonohydroxamate; Reservoir (20% (w/v) PEG-8000, 100 mM Tris pH 8.5, 200 mM MgCl2); Cryoprotection (Reservoir, + 20% glycerol, 50 mM MgCl, 10 mM D-ribonohydroxamate), sitting drop vapor diffuction, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 178.363	α = 90
b = 395.688	β = 90
c = 177.802	γ = 90

Symmetry
Space Group	C 2 2 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	CCD	RAYONIX MX225HE	MIRRORS	2011-07-11	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 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	1.8	197.844	100	0.133	10	6.7	573535	573535

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	1.8	1.9	99.9		0.649	0.649	1.2	5.8	83299

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	THROUGHOUT	3TJ4	1.8	197.84	573175	573175	28777	99.9	0.139	0.139	0.1371	0.1755	RANDOM	17.366

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]
0.81			0.21		-1.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.305
r_dihedral_angle_4_deg	18.887
r_dihedral_angle_3_deg	12.367
r_dihedral_angle_1_deg	6.481
r_angle_refined_deg	1.851
r_angle_other_deg	0.931
r_chiral_restr	0.123
r_bond_refined_d	0.02
r_gen_planes_refined	0.012
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.305
r_dihedral_angle_4_deg	18.887
r_dihedral_angle_3_deg	12.367
r_dihedral_angle_1_deg	6.481
r_angle_refined_deg	1.851
r_angle_other_deg	0.931
r_chiral_restr	0.123
r_bond_refined_d	0.02
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	46512
Nucleic Acid Atoms
Solvent Atoms	5793
Heterogen Atoms	531

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
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 R01GM157729.