3K3H | pdb_00003k3h

Crystal structure of the PDE9A catalytic domain in complex with (S)-BAY73-6691

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3K3E	PDB entry 3K3E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277	soaking PDE9A2-IBMX crystal in the buffer of 0.1 M HEPES pH 7.5, 3.6 M sodium formate, and 2 mM S6691 at 25 deg C for 3 days. The PDE9A2-IBMX crystals were grown by (1) mixing 10-15 mg/mL PDE9A2 catalytic domain (amino acids 181-506) with 2 mM IBMX in a buffer of 50 mM NaCl, 20 mM Tris-HCl pH 7.5, 1 mM beta-mercaptoethanol, 1 mM EDTA, and (2) the vapor diffusion (hanging drop) at 4 deg C. The protein drops contained 2 microliters PDE9A2-IBMX complex and 2 microliters well solution of 0.1 M HEPES pH 7.5 and 3.0 M sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
4.69	73.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.272	α = 90
b = 103.272	β = 90
c = 271.098	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		2009-06-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.1000	NSLS	X29A

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	2.5	30	99.9	0.081	0.081	12.6	11.3		51787

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	2.5	2.6	100		0.57	4.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	MOLECULAR REPLACEMENT	PDB entry 3K3E	2.5	30	51708	49441	4982	95.6	0.223	0.223	0.2186	0.2453	0.2409	random	51.5

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	5288
Nucleic Acid Atoms
Solvent Atoms	16
Heterogen Atoms	52

Software

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