1XM6

Catalytic Domain Of Human Phosphodiesterase 4B In Complex With (R)-Mesopram


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP10277ammonium sulfate and lithium sulfate , pH 10.0, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K
Crystal Properties
Matthews coefficientSolvent content
2.4148.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.221α = 90
b = 94.062β = 90
c = 105.236γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDADSC QUANTUM 2102003-07-31MSINGLE 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
11.9270.7199.70.0676.276460164601
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)
11.921.971000.7861.56.34949

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 REPLACEMENTTHROUGHOUT1.9270.716460164601342799.710.202290.201010.22673RANDOM25.182
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]
-1.54-1.573.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg3.053
r_scangle_it3.039
r_scbond_it1.863
r_angle_refined_deg1.414
r_mcangle_it1.112
r_angle_other_deg1.03
r_mcbond_it0.584
r_symmetry_vdw_other0.297
r_symmetry_vdw_refined0.267
r_nbd_other0.225
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg3.053
r_scangle_it3.039
r_scbond_it1.863
r_angle_refined_deg1.414
r_mcangle_it1.112
r_angle_other_deg1.03
r_mcbond_it0.584
r_symmetry_vdw_other0.297
r_symmetry_vdw_refined0.267
r_nbd_other0.225
r_nbd_refined0.216
r_xyhbond_nbd_refined0.123
r_symmetry_hbond_refined0.112
r_nbtor_other0.105
r_chiral_restr0.089
r_metal_ion_refined0.053
r_bond_refined_d0.012
r_gen_planes_refined0.011
r_gen_planes_other0.007
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 Atoms5467
Nucleic Acid Atoms
Solvent Atoms224
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
ELVESdata scaling
EPMRphasing