1XMU

Catalytic Domain Of Human Phosphodiesterase 4B In Complex With Roflumilast


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP10277ammonium sulfate and lithium sulfate , pH 10, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4850.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.316α = 90
b = 94.1β = 90
c = 108.026γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDADSC QUANTUM 2102004-06-10MSINGLE 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
12.370.7190.910.0677.94.73552435524
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)
12.32.36940.5682.34.42803

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 REPLACEMENTTHROUGHOUT2.370.713552435524187490.910.209860.207970.24556RANDOM32.301
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]
-1.251.71-0.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg3.034
r_scangle_it2.967
r_scbond_it1.776
r_angle_refined_deg1.394
r_mcangle_it1.139
r_angle_other_deg1.048
r_mcbond_it0.581
r_symmetry_vdw_other0.32
r_nbd_other0.217
r_nbd_refined0.212
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg3.034
r_scangle_it2.967
r_scbond_it1.776
r_angle_refined_deg1.394
r_mcangle_it1.139
r_angle_other_deg1.048
r_mcbond_it0.581
r_symmetry_vdw_other0.32
r_nbd_other0.217
r_nbd_refined0.212
r_symmetry_vdw_refined0.161
r_xyhbond_nbd_refined0.15
r_symmetry_hbond_refined0.126
r_nbtor_other0.099
r_chiral_restr0.089
r_metal_ion_refined0.072
r_bond_refined_d0.013
r_gen_planes_refined0.009
r_gen_planes_other0.004
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 Atoms5307
Nucleic Acid Atoms
Solvent Atoms79
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
ELVESdata scaling
EPMRphasing