3MF0

Crystal structure of PDE5A GAF domain (89-518)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.6298The unliganded PDE5A1C149S (20 mg/mL) was crystallized by vapor diffusion against the well buffer of 10% PEG3350, 5% MPD, 0.1 M sodium citrate, pH5.6, 20 mM DTT. , VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
4.1770.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 144.534α = 90
b = 144.534β = 90
c = 135.008γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MMAD
21x-rayMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.08NSLSX29A
2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1,23.1301000.1289.51129794
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
3.13.21002.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3.13028228150799.480.235050.232190.28865RANDOM100.54
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]
-1.69-0.85-1.692.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.389
r_dihedral_angle_3_deg27.946
r_dihedral_angle_4_deg21.659
r_dihedral_angle_1_deg14.257
r_scangle_it8.826
r_scbond_it5.417
r_mcangle_it4.224
r_mcbond_it2.334
r_angle_refined_deg1.319
r_chiral_restr0.106
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.389
r_dihedral_angle_3_deg27.946
r_dihedral_angle_4_deg21.659
r_dihedral_angle_1_deg14.257
r_scangle_it8.826
r_scbond_it5.417
r_mcangle_it4.224
r_mcbond_it2.334
r_angle_refined_deg1.319
r_chiral_restr0.106
r_gen_planes_refined0.023
r_bond_refined_d0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5921
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
ADSCdata collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling