3FKK | pdb_00003fkk

Structure of L-2-keto-3-deoxyarabonate dehydratase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	50mM Tris-HCl,5% 2-propanol, 0.4M Ammonium phospate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.911	α = 90
b = 78.911	β = 90
c = 207.712	γ = 120

Symmetry
Space Group	P 31 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		CCD	RIGAKU JUPITER 210			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.0	SPring-8	BL38B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	48.8	94.6				48899		29.2	10.1

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	SAD	THROUGHOUT	2.1	15	43627	4430	97.9	0.184	0.184	0.18	0.216	0.22	RANDOM	16.1

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]
2.07	1.32		2.07		-4.14

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	21.7
c_scangle_it	3.11
c_scbond_it	2.17
c_mcangle_it	1.68
c_angle_deg	1.3
c_mcbond_it	1.15
c_improper_angle_d	0.79
c_bond_d	0.005
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4682
Nucleic Acid Atoms
Solvent Atoms	445
Heterogen Atoms	10

Software

Software
Software Name	Purpose
HKL-2000	data collection
SHELXS	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling