4NP7

Structure of phosphotriesterase mutant (S308L/Y309A) from Agrobacterium radiobacter with diethyl thiophosphate bound in the active site


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP727720% PEG3350, 0.2M NANO3, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.0659.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.134α = 90
b = 109.134β = 90
c = 63.428γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2013-02-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEOTHER1.5418

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
11.9928.2299.80.12315.47.23026030260
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)
11.992.0498.40.8892.46.630260

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2D2J1.9928.222831728317151098.330.207990.207990.205670.25108RANDOM23.797
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]
-0.01-0.01-0.010.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.656
r_dihedral_angle_4_deg16.485
r_dihedral_angle_3_deg14.954
r_dihedral_angle_1_deg6.223
r_long_range_B_refined5.556
r_long_range_B_other5.482
r_scangle_other4.24
r_mcangle_it3.023
r_mcangle_other3.022
r_scbond_it2.868
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.656
r_dihedral_angle_4_deg16.485
r_dihedral_angle_3_deg14.954
r_dihedral_angle_1_deg6.223
r_long_range_B_refined5.556
r_long_range_B_other5.482
r_scangle_other4.24
r_mcangle_it3.023
r_mcangle_other3.022
r_scbond_it2.868
r_scbond_other2.866
r_mcbond_it2.07
r_mcbond_other2.07
r_angle_refined_deg2.036
r_angle_other_deg0.947
r_chiral_restr0.119
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2506
Nucleic Acid Atoms
Solvent Atoms159
Heterogen Atoms15

Software

Software
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
Aimlessdata scaling