1XVI

Crystal Structure of YedP, phosphatase-like domain protein from Escherichia coli K12

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	295	PEG 8000, ammonium sulfate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.783	α = 90
b = 79.975	β = 99.56
c = 75.471	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	SBC-3	mirrors	2004-05-30	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	SBC-3	mirrors	2004-05-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.98016	APS	19-BM
2	SYNCHROTRON	APS BEAMLINE 19-BM	0.98032	APS	19-BM

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	2.26	74.33	99.4	0.06	7	4.1	30945	30085

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)
	2.26	2.35	95.4		0.219	3.9	3.8	2868

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.26	74.33	26247	26247	2964	96.8	0.19	0.19	0.18388	0.24334	RANDOM	32.188

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]
0.12		-1.26	-0.08		-0.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.604
r_dihedral_angle_3_deg	17.14
r_dihedral_angle_4_deg	13.607
r_dihedral_angle_1_deg	6.303
r_scangle_it	2.95
r_scbond_it	1.864
r_mcangle_it	1.593
r_angle_refined_deg	1.408
r_mcbond_it	0.913
r_nbd_refined	0.203
r_xyhbond_nbd_refined	0.189
r_symmetry_hbond_refined	0.179
r_symmetry_vdw_refined	0.176
r_chiral_restr	0.093
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_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	3724
Nucleic Acid Atoms
Solvent Atoms	388
Heterogen Atoms	54

Software

Software
Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data scaling
SHARP	phasing