5GZ5

Crystal structure of snake venom phosphodiesterase (PDE) from Taiwan cobra (Naja atra atra) in complex with AMP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5GZ4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.1M Imidazole pH6.5, 0.2M Zinc acetate, 20% PEG 3000, 1mM AMP

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 171.207	α = 90
b = 65.612	β = 90
c = 88.675	γ = 90

Symmetry
Space Group	P 21 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	200	CCD	RAYONIX MX300HE		2016-03-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL15A1	1.0	NSRRC	BL15A1

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	2.09	30	99.1	0.059	22.5	4.8		59141

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.18

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5GZ4	2.093	27.876	1.37	58941	2923	98.72	0.1803	0.1783	0.2187

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	17.229
f_angle_d	1.29
f_chiral_restr	0.064
f_bond_d	0.013
f_plane_restr	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6232
Nucleic Acid Atoms
Solvent Atoms	807
Heterogen Atoms	180

Software

Software
Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

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.