3KOX | pdb_00003kox

Crystal Structure of ornithine 4,5 aminomutase in complex with 2,4-diaminobutyrate (Anaerobic)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8	294	A protein solution (8 mg/ml 4,5-OAM, 5 mM 2-mercaptoethanol, 10 mM Tris HCl pH 8.0, 2 mM PLP, and 2 mM AdoCbl) was mixed in a 1:1 ratio with precipitant solution [(0.1 M Tris HCl, pH 8.0, 0.2 M MgCl2, 25% (wt/vol) polyethylene glycol 2000 mono-methylether] under redlight at room temperature, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.96	α = 90
b = 231.69	β = 103.16
c = 123.89	γ = 90

Symmetry
Space Group	P 1 21 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		2009-04-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02		Diamond	I02

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	2.4	65	99.9	0.097	9			133606		1

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	2.4	2.46	99.9		0.377	2.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	FOURIER SYNTHESIS	THROUGHOUT	2.4	64.23	133606	7055	99.9	0.193	0.19	0.19	0.257	0.25	RANDOM	24.22

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]
0.01		-0.24	0.25		-0.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.835
r_dihedral_angle_4_deg	17.906
r_dihedral_angle_3_deg	17.637
r_dihedral_angle_1_deg	6.746
r_scangle_it	3.281
r_scbond_it	2.03
r_angle_refined_deg	1.795
r_mcangle_it	1.245
r_angle_other_deg	0.988
r_mcbond_it	0.666
r_chiral_restr	0.185
r_mcbond_other	0.137
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	26064
Nucleic Acid Atoms
Solvent Atoms	787
Heterogen Atoms	528

Software

Software
Software Name	Purpose
DNA	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling