5EQV

1.45 Angstrom Crystal Structure of Bifunctional 2',3'-cyclic Nucleotide 2'-phosphodiesterase/3'-Nucleotidase Periplasmic Precursor Protein from Yersinia pestis with Phosphate bound to the Active site

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	295	Protein: 8.6 mg/ml, 0.01M Tris-HCL (pH 8.3), 5mM Thymidine; Screen: Classics II (F11), 0.2M Sodium chloride, 0.1M Bis-Tris (pH 6.5), 25% (w/v) PEG 3350;

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.282	α = 90
b = 107.282	β = 90
c = 63.357	γ = 90

Symmetry
Space Group	P 43 21 2

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	MARMOSAIC 325 mm CCD		2015-10-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.45	30	100	0.054	0.054	42.6	12.6		65853		-3	17.4

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	1.45	1.48	100		0.545	5.3	12.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB3JYF	1.45	29.91	62495	3280	99.92	0.13301	0.13195	0.15302	RANDOM	21.268

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]
-1.07			-1.07		2.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.575
r_dihedral_angle_4_deg	21.022
r_dihedral_angle_3_deg	10.691
r_sphericity_bonded	9.502
r_long_range_B_refined	7.111
r_long_range_B_other	6.229
r_dihedral_angle_1_deg	5.205
r_rigid_bond_restr	4.585
r_scangle_other	2.449
r_scbond_it	1.562
r_scbond_other	1.556
r_angle_refined_deg	1.477
r_mcangle_other	1.477
r_mcangle_it	1.475
r_mcbond_it	0.946
r_mcbond_other	0.939
r_angle_other_deg	0.913
r_chiral_restr	0.105
r_gen_planes_refined	0.023
r_gen_planes_other	0.019
r_bond_refined_d	0.01
r_bond_other_d	0.002
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_scangle_it
r_sphericity_free

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2592
Nucleic Acid Atoms
Solvent Atoms	629
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing
BLU-MAX	data collection