3DYQ

human phosphodiestrase 9 (inhibited by omitting divalent cation) in complex with cGMP

X-RAY DIFFRACTION

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Crystallization

Crystal Properties
Matthews coefficient	Solvent content
4.66	73.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.65	α = 90
b = 103.65	β = 90
c = 270.041	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					M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.0	APS	17-ID

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	98.7	0.085	23	7		65299		2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 1TBM	2.5	50	46414	5261	99.54	0.19885	0.19566	0.22627	RANDOM	40.023

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]
1.86			1.86		-3.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.991
r_dihedral_angle_4_deg	21.603
r_dihedral_angle_3_deg	17.57
r_dihedral_angle_1_deg	6.529
r_scangle_it	4.327
r_scbond_it	2.76
r_mcangle_it	1.499
r_angle_refined_deg	1.35
r_angle_other_deg	0.832
r_mcbond_it	0.717
r_symmetry_vdw_other	0.3
r_symmetry_vdw_refined	0.27
r_symmetry_hbond_refined	0.268
r_nbd_refined	0.262
r_nbd_other	0.213
r_xyhbond_nbd_refined	0.207
r_metal_ion_refined	0.203
r_nbtor_refined	0.201
r_mcbond_other	0.187
r_nbtor_other	0.092
r_chiral_restr	0.077
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_xyhbond_nbd_other
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	238
Heterogen Atoms	43

Software

Software
Software Name	Purpose
REFMAC	refinement