2A5H | pdb_00002a5h

2.1 Angstrom X-ray crystal structure of lysine-2,3-aminomutase from Clostridium subterminale SB4, with Michaelis analog (L-alpha-lysine external aldimine form of pyridoxal-5'-phosphate).

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	300	sodium N-2-hydroxy-ethylpiperazine-N'--3-propage sulfonic acid (EPPS, or HEPPS), sodium malonaate, L-alpha-lysine, dithiothreitol, polyethylene glycol 200, polyethylene glycol 8000, s-adenosylmethionine, iron-II-sulfate, , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 300K
2	VAPOR DIFFUSION, HANGING DROP	8	300	sodium N-2-hydroxy-ethylpiperazine-N'--3-propage sulfonic acid (EPPS, or HEPPS), sodium malonaate, L-alpha-lysine, dithiothreitol, polyethylene glycol 200, polyethylene glycol 8000, s-adenosylmethionine, iron-II-sulfate, , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.89	α = 90
b = 92.926	β = 96.74
c = 177.735	γ = 90

Symmetry
Space Group	C 1 2 1

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	ADSC QUANTUM 315	monochromator with Si (111) crystal	2003-04-09	M	SINGLE WAVELENGTH
2	2	x-ray	100	CCD	ADSC QUANTUM 4	monochromator with Si(111) double-crystal	2003-03-28	M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	0.9742	NSLS	X25
2	SYNCHROTRON	APS BEAMLINE 17-ID	0.9792	APS	17-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	2.1	50	81.53	0.103	0.103	2	3	83957	83957

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	2.1	2.18	62.3		0.265	0.265	2.97	2.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	SAD	THROUGHOUT	2.1	50	83957	83957	7437	81.53	0.18732	0.18396	0.2661	0.22485	0.2922	RANDOM	33.824

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]
0.3		-1.71	3.3		-4.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.993
r_dihedral_angle_4_deg	20.774
r_dihedral_angle_3_deg	20.343
r_dihedral_angle_1_deg	7.18
r_angle_refined_deg	3.086
r_scangle_it	2.362
r_scbond_it	1.635
r_mcangle_it	0.861
r_mcbond_it	0.582
r_symmetry_hbond_refined	0.393
r_symmetry_vdw_refined	0.382
r_nbtor_refined	0.317
r_nbd_refined	0.232
r_chiral_restr	0.177
r_xyhbond_nbd_refined	0.164
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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	12990
Nucleic Acid Atoms
Solvent Atoms	608
Heterogen Atoms	264

Software

Software
Software Name	Purpose
REFMAC	refinement
CBASS	data collection
MX	data reduction
JBluIce-EPICS	data collection
SCALEPACK	data scaling
SOLVE	phasing