1XOS

Catalytic Domain Of Human Phosphodiesterase 4B In Complex With Sildenafil


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP10277ammonium sulfate and lithium sulfate , pH 10.0, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K
Crystal Properties
Matthews coefficientSolvent content
2.4750.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.571α = 90
b = 107.117β = 90
c = 89.481γ = 90
Symmetry
Space GroupI 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDADSC QUANTUM 2102003-05-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.1ALS8.3.1

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
12.2870.7199.70.0716.85.21991619916
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.282.3391000.010841.65.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.2870.711991619916108099.680.212450.210090.25683RANDOM43.618
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]
1.984.68-6.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.138
r_scangle_it3.185
r_scbond_it1.996
r_angle_refined_deg1.538
r_mcangle_it1.337
r_angle_other_deg1.099
r_mcbond_it0.711
r_symmetry_vdw_other0.343
r_symmetry_vdw_refined0.253
r_nbd_other0.223
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.138
r_scangle_it3.185
r_scbond_it1.996
r_angle_refined_deg1.538
r_mcangle_it1.337
r_angle_other_deg1.099
r_mcbond_it0.711
r_symmetry_vdw_other0.343
r_symmetry_vdw_refined0.253
r_nbd_other0.223
r_nbd_refined0.215
r_xyhbond_nbd_refined0.16
r_nbtor_other0.112
r_metal_ion_refined0.103
r_symmetry_hbond_refined0.096
r_chiral_restr0.091
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_gen_planes_other0.005
r_bond_other_d0.002
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_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 AtomsNumber
Protein Atoms2597
Nucleic Acid Atoms
Solvent Atoms17
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
ELVESdata scaling
EPMRphasing