4MYQ

Selective Inhibition of the Catalytic Domain Of Human Phosphodiesterase 4B With A-33


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5289VCID6271 PDE4 AT 7.9 MG/ML IN 20MM HEPES PH 7.5, 100 MM NACL, 1MM DTT, WITH 0.5MM A-33 AGAINST JCSG_ A10 (OPTIMIZATION SCREEN), 328.57MM POTASSIUM FORMATE, 24% W/V PEG 3350, CRYO 20% ETHYLENE GLYCOL AND 0.1MM COMPOUND, CRYSTAL TRACKING ID 232128E12, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K, temperature 289.0K
Crystal Properties
Matthews coefficientSolvent content
2.7354.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.7α = 90
b = 99.7β = 90
c = 47.02γ = 90
Symmetry
Space GroupP 42

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2012-03-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
11.949.8597.30.08712.53.236759357592-318.71
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)
11.91.9586.70.4832.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 REPLACEMENTTHROUGHOUTPDB entry 3G451.949.8523675935759178897.30.190.1880.222RANDOM12.8
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]
0.120.12-0.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.805
r_dihedral_angle_4_deg19.018
r_dihedral_angle_3_deg13.778
r_dihedral_angle_1_deg5.002
r_angle_refined_deg1.487
r_angle_other_deg1.013
r_chiral_restr0.084
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_gen_planes_other0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.805
r_dihedral_angle_4_deg19.018
r_dihedral_angle_3_deg13.778
r_dihedral_angle_1_deg5.002
r_angle_refined_deg1.487
r_angle_other_deg1.013
r_chiral_restr0.084
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_gen_planes_other0.006
r_bond_other_d0.003
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_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2758
Nucleic Acid Atoms
Solvent Atoms375
Heterogen Atoms41

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling