1Y2K | pdb_00001y2k

Catalytic Domain Of Human Phosphodiesterase 4D In Complex With 3,5-dimethyl-1-(3-nitro-phenyl)-1H-pyrazole-4-carboxylic acid ethyl ester


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7288PEG3350, ethylene glycol, isopropanol, glycerol and DTT , pH 6.0-8.5, VAPOR DIFFUSION, SITTING DROP, temperature 288K, pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.4349.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.349α = 90
b = 78.886β = 90
c = 164.01γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDADSC QUANTUM 210MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.1ALS8.3.1

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
11.3681.6590.10.059.24143297143297
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)
11.361.39586.40.5171.73.110588

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.3681.65143297143297753689.630.175210.175210.174560.180.187650.2RANDOM10.441
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]
0.55-0.36-0.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg2.719
r_scangle_it2.151
r_scbond_it1.284
r_angle_refined_deg1.06
r_angle_other_deg0.786
r_mcangle_it0.724
r_mcbond_it0.357
r_symmetry_vdw_other0.272
r_nbd_other0.222
r_nbd_refined0.208
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg2.719
r_scangle_it2.151
r_scbond_it1.284
r_angle_refined_deg1.06
r_angle_other_deg0.786
r_mcangle_it0.724
r_mcbond_it0.357
r_symmetry_vdw_other0.272
r_nbd_other0.222
r_nbd_refined0.208
r_symmetry_hbond_refined0.111
r_xyhbond_nbd_refined0.104
r_nbtor_other0.081
r_symmetry_vdw_refined0.078
r_chiral_restr0.071
r_bond_refined_d0.006
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5253
Nucleic Acid Atoms
Solvent Atoms459
Heterogen Atoms178

Software

Software
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
ELVESdata scaling
EPMRphasing