1Y2J | pdb_00001y2j

Catalytic Domain Of Human Phosphodiesterase 4B 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 DROP10277ammonium sulfate and lithium sulfate , pH 10, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4650.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.484α = 90
b = 94.235β = 90
c = 106.843γ = 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
12.5570.7184.460.1015.14.12412824128
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)
12.552.61689.80.5691.841917

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 REPLACEMENTTHROUGHOUT2.5570.712412824128128584.460.246270.246270.243640.2430.297410.2925RANDOM16.287
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]
-5.57-2.027.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg2.966
r_scangle_it2.48
r_scbond_it1.525
r_angle_refined_deg1.513
r_mcangle_it0.944
r_angle_other_deg0.936
r_mcbond_it0.485
r_symmetry_vdw_other0.29
r_symmetry_vdw_refined0.275
r_nbd_refined0.222
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg2.966
r_scangle_it2.48
r_scbond_it1.525
r_angle_refined_deg1.513
r_mcangle_it0.944
r_angle_other_deg0.936
r_mcbond_it0.485
r_symmetry_vdw_other0.29
r_symmetry_vdw_refined0.275
r_nbd_refined0.222
r_nbd_other0.217
r_xyhbond_nbd_refined0.192
r_metal_ion_refined0.109
r_nbtor_other0.096
r_chiral_restr0.091
r_symmetry_hbond_refined0.04
r_bond_refined_d0.014
r_gen_planes_refined0.007
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 Atoms5234
Nucleic Acid Atoms
Solvent Atoms56
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
ELVESdata scaling
EPMRphasing