1TB5 | pdb_00001tb5

Catalytic Domain Of Human Phosphodiesterase 4B In Complex With AMP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP10277ammonium sulfate, lithium sulfate, pH 10, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.5852.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.547α = 90
b = 94.241β = 90
c = 107.243γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDADSC QUANTUM 2102003-08-28MSINGLE 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
12.1570.710.0799.24.74698846988
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)
12.152.2061000.7511.634.7

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 (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.1570.714698846988250598.910.235440.233620.240.268220.27RANDOM29.352
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]
-3.60.842.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg3.214
r_scangle_it3.092
r_scbond_it1.974
r_angle_refined_deg1.502
r_mcangle_it1.113
r_angle_other_deg0.937
r_mcbond_it0.606
r_symmetry_vdw_other0.313
r_nbd_other0.222
r_nbd_refined0.221
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg3.214
r_scangle_it3.092
r_scbond_it1.974
r_angle_refined_deg1.502
r_mcangle_it1.113
r_angle_other_deg0.937
r_mcbond_it0.606
r_symmetry_vdw_other0.313
r_nbd_other0.222
r_nbd_refined0.221
r_xyhbond_nbd_refined0.178
r_symmetry_hbond_refined0.177
r_symmetry_vdw_refined0.143
r_metal_ion_refined0.121
r_chiral_restr0.096
r_nbtor_other0.093
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_gen_planes_other0.008
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 Atoms5226
Nucleic Acid Atoms
Solvent Atoms69
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
ELVESdata scaling
EPMRphasing