5LBO | pdb_00005lbo

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-001


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3SL3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529324% PEG 3350, 30% Ethylene Glycol, 0.1 M HEPES
Crystal Properties
Matthews coefficientSolvent content
2.6353.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.223α = 90
b = 111.092β = 90
c = 160.798γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6MCRL2016-04-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97623DiamondI03

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
12.25160.896.40.1130.99813.86.580611
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)
12.252.381000.7632.66.5

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3SL32.2591.476504402396.370.17540.173650.180.209650.21RANDOM45.341
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]
1.17-2.191.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.563
r_dihedral_angle_4_deg20.26
r_dihedral_angle_3_deg15.572
r_long_range_B_refined9.564
r_long_range_B_other9.564
r_scangle_other7.753
r_mcangle_it5.325
r_mcangle_other5.325
r_scbond_it5.185
r_scbond_other5.184
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.563
r_dihedral_angle_4_deg20.26
r_dihedral_angle_3_deg15.572
r_long_range_B_refined9.564
r_long_range_B_other9.564
r_scangle_other7.753
r_mcangle_it5.325
r_mcangle_other5.325
r_scbond_it5.185
r_scbond_other5.184
r_dihedral_angle_1_deg5.18
r_mcbond_it3.795
r_mcbond_other3.795
r_angle_refined_deg1.699
r_angle_other_deg1.649
r_chiral_restr0.104
r_bond_refined_d0.015
r_bond_other_d0.01
r_gen_planes_refined0.01
r_gen_planes_other0.008
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10526
Nucleic Acid Atoms
Solvent Atoms553
Heterogen Atoms360

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing