1XOQ

Catalytic Domain Of Human Phosphodiesterase 4D In Complex With Roflumilast


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7288PEG3350, ethylene glycol, isopropanol, glycerol and DTT , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 288K
Crystal Properties
Matthews coefficientSolvent content
2.4249.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.899α = 90
b = 60.116β = 90
c = 163.996γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDADSC QUANTUM 2102004-03-31MSINGLE 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
11.8381.6596.850.0581.93.16404864048
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.831.87890.40.5082.44473

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 REPLACEMENTTHROUGHOUT1.8381.656404864048340296.850.178060.176650.20469RANDOM8.756
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]
-0.050.98-0.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg2.73
r_scangle_it2.527
r_scbond_it1.532
r_angle_refined_deg1.261
r_angle_other_deg0.96
r_mcangle_it0.834
r_mcbond_it0.428
r_symmetry_vdw_other0.332
r_nbd_other0.23
r_nbd_refined0.207
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg2.73
r_scangle_it2.527
r_scbond_it1.532
r_angle_refined_deg1.261
r_angle_other_deg0.96
r_mcangle_it0.834
r_mcbond_it0.428
r_symmetry_vdw_other0.332
r_nbd_other0.23
r_nbd_refined0.207
r_symmetry_hbond_refined0.155
r_symmetry_vdw_refined0.151
r_xyhbond_nbd_refined0.132
r_chiral_restr0.097
r_nbtor_other0.083
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_gen_planes_other0.006
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_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 AtomsNumber
Protein Atoms5253
Nucleic Acid Atoms
Solvent Atoms360
Heterogen Atoms152

Software

Software
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
ELVESdata scaling
EPMRphasing