3JYF | pdb_00003jyf

The crystal structure of a 2,3-cyclic nucleotide 2-phosphodiesterase/3-nucleotidase bifunctional periplasmic precursor protein from Klebsiella pneumoniae subsp. pneumoniae MGH 78578

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	0.1M Tris pH8.5, 2.5M Ammonium sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.44	64.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.041	α = 90
b = 106.041	β = 90
c = 182.967	γ = 90

Symmetry
Space Group	P 41 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	SBC-3	mirror	2009-04-18	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.97954, 0.97986	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	2.43	50	99.8	0.146	33.44	9.7	40035	40035

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	2.43	2.47	96.1		0.767	4.41	7.7	1896

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	MAD	THROUGHOUT	2.43	50	37255	1965	97.95	0.18171	0.17915	0.1869	0.23079	0.23	RANDOM	31.654

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]
-1.16			-1.16		2.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.667
r_dihedral_angle_4_deg	20.381
r_dihedral_angle_3_deg	14.683
r_dihedral_angle_1_deg	5.913
r_scangle_it	3.176
r_scbond_it	1.875
r_angle_refined_deg	1.297
r_mcangle_it	1.177
r_mcbond_it	0.602
r_chiral_restr	0.091

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.667
r_dihedral_angle_4_deg	20.381
r_dihedral_angle_3_deg	14.683
r_dihedral_angle_1_deg	5.913
r_scangle_it	3.176
r_scbond_it	1.875
r_angle_refined_deg	1.297
r_mcangle_it	1.177
r_mcbond_it	0.602
r_chiral_restr	0.091
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5121
Nucleic Acid Atoms
Solvent Atoms	492
Heterogen Atoms	114

Software

Software
Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
ARP	model building
WARP	model building
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.