1Y2H

Catalytic Domain Of Human Phosphodiesterase 4B In Complex With 1-(2-chloro-phenyl)-3,5-dimethyl-1H-pyrazole-4-carboxylic acid ethyl ester


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
2.4650.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.541α = 90
b = 94.178β = 90
c = 106.819γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDADSC QUANTUM 210MSINGLE 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
12.470.7199.450.0727.34.63395533955
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)
12.42.4621000.8781.44.62582

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.470.713395533955177999.450.247620.247620.244960.29933RANDOM33.214
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]
-6.130.565.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg2.583
r_scangle_it1.748
r_angle_refined_deg1.198
r_scbond_it1.057
r_angle_other_deg0.873
r_mcangle_it0.663
r_mcbond_it0.349
r_metal_ion_refined0.225
r_symmetry_vdw_other0.215
r_nbd_other0.205
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg2.583
r_scangle_it1.748
r_angle_refined_deg1.198
r_scbond_it1.057
r_angle_other_deg0.873
r_mcangle_it0.663
r_mcbond_it0.349
r_metal_ion_refined0.225
r_symmetry_vdw_other0.215
r_nbd_other0.205
r_nbd_refined0.195
r_symmetry_vdw_refined0.167
r_xyhbond_nbd_refined0.129
r_symmetry_hbond_refined0.114
r_nbtor_other0.094
r_chiral_restr0.072
r_bond_refined_d0.01
r_gen_planes_refined0.006
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 Atoms5234
Nucleic Acid Atoms
Solvent Atoms44
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
ELVESdata scaling
EPMRphasing