5LAQ | pdb_00005laq

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3G45 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.629350 mM calcium acetate, 20% PEG 400, 100 mM sodium acetate
Crystal Properties
Matthews coefficientSolvent content
2.3547.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.737α = 90
b = 95.737β = 90
c = 85.113γ = 120
Symmetry
Space GroupP 31 2 1

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
12.482.911000.1290.998138.517941
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)
12.42.531000.782.36.1

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 REPLACEMENTTHROUGHOUT3G452.482.911716674499.940.174080.171130.180.240840.25RANDOM51.062
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]
1.030.511.03-3.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.611
r_dihedral_angle_4_deg24.417
r_dihedral_angle_3_deg15.509
r_long_range_B_refined8.679
r_long_range_B_other8.678
r_scangle_other7.065
r_dihedral_angle_1_deg5.914
r_mcangle_it5.243
r_mcangle_other5.243
r_scbond_it4.552
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.611
r_dihedral_angle_4_deg24.417
r_dihedral_angle_3_deg15.509
r_long_range_B_refined8.679
r_long_range_B_other8.678
r_scangle_other7.065
r_dihedral_angle_1_deg5.914
r_mcangle_it5.243
r_mcangle_other5.243
r_scbond_it4.552
r_scbond_other4.551
r_mcbond_it3.589
r_mcbond_other3.566
r_angle_refined_deg1.582
r_angle_other_deg1
r_chiral_restr0.088
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms2720
Nucleic Acid Atoms
Solvent Atoms85
Heterogen Atoms57

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing