6RCW | pdb_00006rcw

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-053


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 pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.6553.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.894α = 90
b = 110.505β = 90
c = 160.694γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MCRL2016-04-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.976250DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.07160.6999.90.0650.070.0270.9916.26.6107710
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.072.0894.80.7940.8590.3270.7526.8

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 REPLACEMENTTHROUGHOUT3SL32.0891.22102189544399.780.174940.172480.180.22110.23RANDOM44.968
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]
0.4-0.14-0.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.901
r_dihedral_angle_4_deg19.538
r_dihedral_angle_3_deg15.06
r_long_range_B_refined8.76
r_long_range_B_other8.76
r_scangle_other6.977
r_dihedral_angle_1_deg5.951
r_mcangle_it4.919
r_mcangle_other4.919
r_scbond_it4.809
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.901
r_dihedral_angle_4_deg19.538
r_dihedral_angle_3_deg15.06
r_long_range_B_refined8.76
r_long_range_B_other8.76
r_scangle_other6.977
r_dihedral_angle_1_deg5.951
r_mcangle_it4.919
r_mcangle_other4.919
r_scbond_it4.809
r_scbond_other4.809
r_mcbond_it3.806
r_mcbond_other3.803
r_angle_refined_deg1.653
r_angle_other_deg1.377
r_chiral_restr0.079
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms10524
Nucleic Acid Atoms
Solvent Atoms658
Heterogen Atoms338

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing