1Y2E | pdb_00001y2e

Catalytic Domain Of Human Phosphodiesterase 4D In Complex With 1-(4-amino-phenyl)-3,5-dimethyl-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 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 288K
Crystal Properties
Matthews coefficientSolvent content
2.4850.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.88α = 90
b = 79.442β = 90
c = 164.265γ = 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
12.181.6598.160.1732.734412444124
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)
12.12.15599.20.315233395

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 REPLACEMENTTHROUGHOUT2.181.654412444124235598.160.190.190.188510.20.217850.23RANDOM12.187
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]
-1.763.53-1.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg2.746
r_scangle_it2.356
r_scbond_it1.433
r_angle_refined_deg1.213
r_mcangle_it0.852
r_angle_other_deg0.843
r_mcbond_it0.463
r_symmetry_vdw_other0.293
r_nbd_other0.22
r_nbd_refined0.203
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg2.746
r_scangle_it2.356
r_scbond_it1.433
r_angle_refined_deg1.213
r_mcangle_it0.852
r_angle_other_deg0.843
r_mcbond_it0.463
r_symmetry_vdw_other0.293
r_nbd_other0.22
r_nbd_refined0.203
r_symmetry_vdw_refined0.169
r_symmetry_hbond_refined0.157
r_xyhbond_nbd_refined0.141
r_chiral_restr0.08
r_nbtor_other0.08
r_metal_ion_refined0.033
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_gen_planes_other0.003
r_bond_other_d0.002
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_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 Atoms5237
Nucleic Acid Atoms
Solvent Atoms271
Heterogen Atoms98

Software

Software
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
ELVESdata scaling
EPMRphasing