2DFJ | pdb_00002dfj

Crystal Structure of the Diadenosine Tetraphosphate Hydrolase from Shigella flexneri 2a

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	291	0.1M Bis-Tris, 0.2M Magnesium chloride and 25% PEG 3350, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.4	63.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 167.498	α = 90
b = 54.965	β = 129.14
c = 119.203	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	MARRESEARCH		2005-06-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BSRF BEAMLINE 3W1A	0.9793	BSRF	3W1A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.72	50	99.7	0.123	17	7.1		22410

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)
	2.72	2.82	99.4		0.123	0.469	6	4.6	2233

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 (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.72	38.95	21519	1164	98.33	0.23128	0.23128	0.22924	0.2291	0.26775	RANDOM	37.282

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]
0.08		0.07	-0.02		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.316
r_dihedral_angle_4_deg	22.423
r_dihedral_angle_3_deg	21.049
r_dihedral_angle_1_deg	8.625
r_scangle_it	2.121
r_angle_refined_deg	1.56
r_scbond_it	1.467
r_mcangle_it	0.891
r_mcbond_it	0.781
r_symmetry_vdw_refined	0.322
r_nbtor_refined	0.32
r_nbd_refined	0.256
r_xyhbond_nbd_refined	0.194
r_symmetry_hbond_refined	0.182
r_chiral_restr	0.105
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4147
Nucleic Acid Atoms
Solvent Atoms	162
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing