3K4S

The structure of the catalytic domain of human PDE4d with 4-(3-Butoxy-4-methoxyphenyl)methyl-2-imidazolidone


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Y2BPDB entry 1Y2B

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.62940.5M Ammonium sulphate, 0.1M Sodium citrate pH 5.6, 1.0M Lithium sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
3.2161.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.217α = 90
b = 83.217β = 90
c = 148.766γ = 90
Symmetry
Space GroupP 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Si (111) double crystal monochromator. Kirkpatrick Baez bimorph mirror pair for horizontal and vertical focussing2009-08-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9795DiamondI02

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
12.0546.1599.80.06911.77.4933561230.1
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)
2.052.1299.90.37147.08

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 1Y2B2.0546.1531860169999.820.211330.208710.26155RANDOM38.084
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]
1.571.57-3.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.447
r_dihedral_angle_4_deg18.781
r_dihedral_angle_3_deg15.685
r_dihedral_angle_1_deg5.331
r_scangle_it4.635
r_scbond_it2.897
r_mcangle_it1.746
r_angle_refined_deg1.608
r_mcbond_it0.945
r_chiral_restr0.118
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.447
r_dihedral_angle_4_deg18.781
r_dihedral_angle_3_deg15.685
r_dihedral_angle_1_deg5.331
r_scangle_it4.635
r_scbond_it2.897
r_mcangle_it1.746
r_angle_refined_deg1.608
r_mcbond_it0.945
r_chiral_restr0.118
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2695
Nucleic Acid Atoms
Solvent Atoms268
Heterogen Atoms22

Software

Software
Software NamePurpose
DNAdata collection
PHASERphasing
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling