Experiment: 3QI3

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277	The catalytic domain of the PDE9Q453E mutant (10-15 mg/mL, amino acids 181-506) was stored in a buffer of 50 mM NaCl, 20 mM Tris.HCl pH 7.5, 1 mM beta-mercaptoethanol, and 1 mM EDTA. After mixing with 2 mM IBMX, the PDE9Q453E-IBMX complex was crystallized by hanging drop vapor diffusion against the well buffer of 2.0 M Na formate, 0.1 M HEPES pH 7.5, 5% xylitol at 277K. Crystals of the PDE9Q453E-(S)-BAY73-6691 complex were prepared by soaking PDE9Q453E-IBMX co-crystals in the crystallization buffer plus 2 mM (S)-BAY73-6691 at 398K for 3 days, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.127	α = 90
b = 103.127	β = 90
c = 270.441	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	ADSC QUANTUM 315			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.1	NSLS	X29A

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	2.3	30	95.7	0.092				63252

Refinement

Statistics
Diffraction ID	Structure Solution Method	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	2.3	30	58317	5832		0.222	0.222	0.242	Random

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
c_angle_deg	1.2
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5370
Nucleic Acid Atoms
Solvent Atoms	23
Heterogen Atoms	52

Software

Software
Software Name	Purpose
ADSC	data collection
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.