3JSW

Human PDE9 in complex with selective inhibitor

X-RAY DIFFRACTION

---

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
4.64	73.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.278	α = 90
b = 103.278	β = 90
c = 270.349	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	IMAGE PLATE	RIGAKU RAXIS IV++	Mirror	2005-11-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.5418

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	50	99.7	0.104	23.2		65686	65551		2

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	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 3DYN	2.3	50	2	58843	6633	99.66	0.18288	0.1795	0.21193	RANDOM	38.298

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]
1.28			1.28		-2.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.384
r_dihedral_angle_4_deg	22.347
r_dihedral_angle_3_deg	16.536
r_dihedral_angle_1_deg	6.068
r_scangle_it	2.604
r_mcangle_it	2.347
r_angle_refined_deg	1.993
r_mcbond_it	1.952
r_scbond_it	1.695
r_angle_other_deg	1.016
r_mcbond_other	0.415
r_nbd_refined	0.227
r_symmetry_vdw_refined	0.226
r_symmetry_vdw_other	0.217
r_nbd_other	0.192
r_nbtor_refined	0.189
r_xyhbond_nbd_refined	0.173
r_chiral_restr	0.12
r_nbtor_other	0.097
r_symmetry_hbond_refined	0.09
r_bond_refined_d	0.026
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5412
Nucleic Acid Atoms
Solvent Atoms	302
Heterogen Atoms	56

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing