1XMY

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


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
2.4650.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.67α = 90
b = 94.633β = 90
c = 106.432γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDADSC QUANTUM 2102004-07-20MSINGLE 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
12.470.7199.150.0964.74.13400634006
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.46299.20.7593.72591

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 REPLACEMENTTHROUGHOUT2.470.713400634006179299.150.24540.242640.29805RANDOM22.28
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]
-3.59-1.875.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg3.999
r_scangle_it3.714
r_scbond_it2.491
r_angle_refined_deg2.04
r_mcangle_it1.448
r_angle_other_deg1.055
r_mcbond_it0.832
r_symmetry_vdw_refined0.411
r_symmetry_vdw_other0.256
r_symmetry_hbond_refined0.235
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg3.999
r_scangle_it3.714
r_scbond_it2.491
r_angle_refined_deg2.04
r_mcangle_it1.448
r_angle_other_deg1.055
r_mcbond_it0.832
r_symmetry_vdw_refined0.411
r_symmetry_vdw_other0.256
r_symmetry_hbond_refined0.235
r_nbd_refined0.233
r_nbd_other0.233
r_xyhbond_nbd_refined0.176
r_metal_ion_refined0.162
r_chiral_restr0.119
r_nbtor_other0.096
r_bond_refined_d0.025
r_gen_planes_refined0.009
r_gen_planes_other0.008
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 Atoms5226
Nucleic Acid Atoms
Solvent Atoms61
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
ELVESdata scaling
EPMRphasing