1T9S

Catalytic Domain Of Human Phosphodiesterase 5A in Complex with GMP

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	8.5	277	PEG 4000, lithium sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.5	49.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.969	α = 90
b = 90.872	β = 98.07
c = 68.991	γ = 90

Symmetry
Space Group	P 1 21 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	2	69.01	99.8	0.124	6.4	3.8	48496	48496

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	2.052	99.9		0.558	2.8	3.8	3719

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 (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	2	69.01	48496	48496	2561	99.8	0.17712	0.17527	0.19	0.21235	0.22	RANDOM	8.597

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]
0.69		0.36	-0.53		-0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	2.702
r_scangle_it	2.519
r_scbond_it	1.554
r_angle_refined_deg	1.352
r_mcangle_it	0.842
r_angle_other_deg	0.81
r_mcbond_it	0.42
r_symmetry_vdw_other	0.283
r_nbd_other	0.222
r_nbd_refined	0.204
r_xyhbond_nbd_refined	0.17
r_symmetry_hbond_refined	0.156
r_symmetry_vdw_refined	0.128
r_nbtor_other	0.085
r_chiral_restr	0.075
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5274
Nucleic Acid Atoms
Solvent Atoms	574
Heterogen Atoms	52

Software

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