3G4L

Crystal structure of human phosphodiesterase 4d with roflumilast


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5293100MM HEPES PH 7.5, 35% ETHYLENE GLYCOL, 5% GLYCEROL, 22% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5852.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.665α = 90
b = 111.952β = 90
c = 161.701γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.1ALS5.0.1

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
12.55099.40.115.46.663001
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)
2.52.5997.30.6166

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 REPLACEMENTTHROUGHOUT2.5506292931870.2170.2140.259RANDOM26.63
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]
-0.28-0.190.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.752
r_dihedral_angle_4_deg19.237
r_dihedral_angle_3_deg16.051
r_dihedral_angle_1_deg5.244
r_scangle_it2.157
r_scbond_it1.324
r_angle_refined_deg1.278
r_angle_other_deg1.009
r_mcangle_it0.845
r_symmetry_vdw_refined0.446
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.752
r_dihedral_angle_4_deg19.237
r_dihedral_angle_3_deg16.051
r_dihedral_angle_1_deg5.244
r_scangle_it2.157
r_scbond_it1.324
r_angle_refined_deg1.278
r_angle_other_deg1.009
r_mcangle_it0.845
r_symmetry_vdw_refined0.446
r_mcbond_it0.436
r_symmetry_hbond_refined0.254
r_symmetry_vdw_other0.234
r_chiral_restr0.158
r_xyhbond_nbd_refined0.156
r_mcbond_other0.142
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_gen_planes_other0.006
r_bond_other_d0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10589
Nucleic Acid Atoms
Solvent Atoms189
Heterogen Atoms164

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement