3ABO

Crystal structure of ethanolamine ammonia-lyase from Escherichia coli complexed with CN-Cbl and ethanolamine

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	277	6.0-7.0 % (w/v) PEG 6000, 24-26 % (v/v) glycerol, 5.0 % (v/v) 2-propanol, 0.1 M HEPES-NaOH, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.93	68.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 242.76	α = 90
b = 242.76	β = 90
c = 76.46	γ = 120

Symmetry
Space Group	P 63

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	RIGAKU JUPITER 210	mirrors	2008-07-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.0000	SPring-8	BL38B1

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	2.1	50	97.2	0.096	17.9	6.8	145836	145836

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.15	93.1		4.35	6.3	9228

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	SAD, MR	THROUGHOUT	PDB ENTRY 2QEZ	2.1	47.51	138458	7304	97.15	0.24099	0.23966	0.2663	RANDOM	15.448

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]
-0.73	-0.37		-0.73		1.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.009
r_dihedral_angle_4_deg	20.776
r_dihedral_angle_3_deg	19.292
r_dihedral_angle_1_deg	10.632
r_scangle_it	4.809
r_scbond_it	3.371
r_mcangle_it	1.737
r_mcbond_it	1.129
r_angle_refined_deg	0.866
r_chiral_restr	0.26
r_bond_refined_d	0.013
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10735
Nucleic Acid Atoms
Solvent Atoms	707
Heterogen Atoms	222

Software

Software
Software Name	Purpose
SHARP	phasing
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling