1TBF

Catalytic Domain Of Human Phosphodiesterase 5A in Complex with Sildenafil

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1T9R	PDB ENTRY 1T9R

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	(NH4)2SO4, PEG 400, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.097	α = 90
b = 76.097	β = 90
c = 99.272	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	CCD	ADSC QUANTUM 210		2003-10-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.1	ALS	8.3.1

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	1.3	65.94	99.6	0.067	12.2	6.5	77378	77378

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	1.3	1.334	99.2		0.803	1.4	6.5	5747

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	THROUGHOUT	PDB ENTRY 1T9R	1.3	65.94	77378	77378	4085	99.16	0.1586	0.1586	0.15717	0.24	0.1855	0.26	RANDOM	10.621

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]
-0.32	-0.16		-0.32		0.48

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	8.461
r_scangle_it	5.819
r_dihedral_angle_1_deg	4.326
r_sphericity_bonded	4.158
r_scbond_it	4.018
r_mcangle_it	2.594
r_rigid_bond_restr	2.172
r_angle_refined_deg	2
r_mcbond_it	1.88
r_angle_other_deg	1.485
r_symmetry_vdw_other	0.425
r_symmetry_hbond_refined	0.392
r_symmetry_vdw_refined	0.38
r_nbd_other	0.241
r_nbd_refined	0.236
r_xyhbond_nbd_refined	0.197
r_chiral_restr	0.135
r_nbtor_other	0.093
r_bond_refined_d	0.025
r_gen_planes_other	0.003
r_bond_other_d	0.002
r_gen_planes_refined	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2637
Nucleic Acid Atoms
Solvent Atoms	323
Heterogen Atoms	41

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
ELVES	data scaling
EPMR	phasing