1TAZ | pdb_00001taz

Catalytic Domain Of Human Phosphodiesterase 1B


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.527750% MPD, 100 mM MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.0559.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.232α = 90
b = 87.232β = 90
c = 134.151γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDADSC QUANTUM 2102003-02-15MSINGLE 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
11.7772.550.0479.22.54838248382
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)
11.771.816980.4591.512.5

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 REPLACEMENTTHROUGHOUT1.7772.554838248382260299.660.182280.18170.19120.193190.1848RANDOM23.328
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]
0.990.99-1.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg4.563
r_scangle_it2.826
r_scbond_it1.732
r_mcangle_it1.132
r_angle_refined_deg1.084
r_angle_other_deg0.858
r_mcbond_it0.557
r_symmetry_vdw_other0.248
r_nbd_other0.225
r_nbd_refined0.205
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg4.563
r_scangle_it2.826
r_scbond_it1.732
r_mcangle_it1.132
r_angle_refined_deg1.084
r_angle_other_deg0.858
r_mcbond_it0.557
r_symmetry_vdw_other0.248
r_nbd_other0.225
r_nbd_refined0.205
r_xyhbond_nbd_refined0.129
r_symmetry_hbond_refined0.096
r_nbtor_other0.094
r_symmetry_vdw_refined0.085
r_chiral_restr0.073
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_gen_planes_other0.004
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_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 Atoms2601
Nucleic Acid Atoms
Solvent Atoms207
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
ELVESdata scaling
EPMRphasing