2OTD

The crystal structure of the glycerophosphodiester phosphodiesterase from Shigella flexneri 2a

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.6	298	0.3M KCl, 10% PEG 6000, 15% Glycerol, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.34	63.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.617	α = 90
b = 82.185	β = 90
c = 223.202	γ = 90

Symmetry
Space Group	P 21 21 21

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	mirrors	2006-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97980	APS	19-ID

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	2.6	50	99.71	0.125	19.56	9.2	44142	44014		2	27

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.668	99.2		0.78	1.85	7.6

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.6	40.06	44014	44014	2365	99.71	0.22362	0.22095	0.27567	RANDOM	26.395

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]
0.58			2.34		-2.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.552
r_dihedral_angle_3_deg	19.004
r_dihedral_angle_4_deg	18.905
r_dihedral_angle_1_deg	7.962
r_scangle_it	2.519
r_scbond_it	1.814
r_angle_refined_deg	1.508
r_mcangle_it	1.14
r_mcbond_it	1.004
r_angle_other_deg	0.96
r_symmetry_vdw_refined	0.282
r_symmetry_vdw_other	0.271
r_nbd_refined	0.23
r_symmetry_hbond_refined	0.206
r_nbd_other	0.203
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.172
r_mcbond_other	0.139
r_xyhbond_nbd_other	0.132
r_nbtor_other	0.094
r_chiral_restr	0.081
r_bond_refined_d	0.014
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_metal_ion_refined
r_metal_ion_other
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	7612
Nucleic Acid Atoms
Solvent Atoms	132
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing