3ANY | pdb_00003any

Crystal structure of ethanolamine ammonia-lyase from escherichia coli complexed with CN-CBL and (R)-2-amino-1-propanol

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.3	277	6.0-7.0% (W/V) PEG 4000, 24-26 % (V/V), GLYCEROL, 1.0% (V/V) 2-METHYL-2,4-PENTANEDIOL (MPD), 0.1M IMIDAZOLE-HCL , pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
4.23	70.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 244.073	α = 90
b = 244.073	β = 90
c = 76.98	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	IMAGE PLATE	BRUCKER DIP-6040	MIRRORS	2008-06-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU		SPring-8	BL44XU

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	48	92.9	0.087	13.2	3.3	141897	141897

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.15	91.5		0.443	2.99	3.2

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 3ABR	2.1	47.84	134843	134843	7043	92.79	0.248	0.248	0.246	0.26	0.276	0.29	RANDOM	43.579

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]
0.28	0.14		0.28		-0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.452
r_dihedral_angle_4_deg	19.673
r_dihedral_angle_3_deg	19.312
r_dihedral_angle_1_deg	9.396
r_scangle_it	4
r_scbond_it	2.745
r_mcangle_it	1.419
r_mcbond_it	0.892
r_angle_refined_deg	0.83
r_chiral_restr	0.22
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
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	10760
Nucleic Acid Atoms
Solvent Atoms	711
Heterogen Atoms	192

Software

Software
Software Name	Purpose
BSS	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling