6ZBA | pdb_00006zba

Crystal structure of PDE4D2 in complex with inhibitor LEO39652


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Y2K 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277Protein stored at 20.6 mg/mL in a storage buffer of 50 mM NaCl, 20 mM Tris HCl (pH 7.5), 1 mM TCEP, 1 mM EDTA. Reservoir was 0.1 M HEPES (pH 7.5), 19% PEG3350, 25% ethylene glycol, 5% 2-propanol, 5% glycerol. Drops were microseeded. Apo crystals were soaked with 0.8 mM LEO39652A for 3 days.
Crystal Properties
Matthews coefficientSolvent content
2.754.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.03α = 90
b = 111.866β = 90
c = 159.623γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 9M2019-09-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9159DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.679.9391000.0850.9979.26.6235229
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.631001.4810.42216

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1Y2K1.679.9392350381194799.9380.1630.16160.170.19180.227.135
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]
0.009-0.008-0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.745
r_dihedral_angle_4_deg16.941
r_dihedral_angle_3_deg13.454
r_lrange_it6.874
r_lrange_other6.455
r_dihedral_angle_1_deg5.423
r_scangle_it4.972
r_scangle_other4.971
r_scbond_it3.319
r_scbond_other3.319
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.745
r_dihedral_angle_4_deg16.941
r_dihedral_angle_3_deg13.454
r_lrange_it6.874
r_lrange_other6.455
r_dihedral_angle_1_deg5.423
r_scangle_it4.972
r_scangle_other4.971
r_scbond_it3.319
r_scbond_other3.319
r_mcangle_it2.804
r_mcangle_other2.804
r_mcbond_it2.157
r_mcbond_other2.157
r_angle_refined_deg1.59
r_angle_other_deg1.521
r_nbd_other0.243
r_xyhbond_nbd_refined0.242
r_symmetry_xyhbond_nbd_refined0.233
r_nbd_refined0.231
r_symmetry_nbd_refined0.217
r_symmetry_nbd_other0.18
r_nbtor_refined0.169
r_symmetry_xyhbond_nbd_other0.136
r_chiral_restr0.09
r_symmetry_nbtor_other0.082
r_metal_ion_refined0.024
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10650
Nucleic Acid Atoms
Solvent Atoms1344
Heterogen Atoms260

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing