3WML

Structure of phosphotriesterase mutant (S308L/Y309A) from Agrobacterium radiobacter


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
2.9758.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.996α = 90
b = 108.996β = 90
c = 61.774γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateMirrors2013-02-22MSINGLE 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
11.98729.35599.80.12220.210.82938629366
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)
11.992.0499.80.7549.929386

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2D2J1.9929.3552787227872149499.820.15820.15820.156680.18672RANDOM19.483
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]
-0.09-0.09-0.090.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.965
r_dihedral_angle_4_deg15.924
r_dihedral_angle_3_deg13.423
r_dihedral_angle_1_deg6.478
r_long_range_B_refined5.152
r_long_range_B_other5.112
r_scangle_other4.188
r_scbond_it2.786
r_scbond_other2.784
r_mcangle_it2.378
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.965
r_dihedral_angle_4_deg15.924
r_dihedral_angle_3_deg13.423
r_dihedral_angle_1_deg6.478
r_long_range_B_refined5.152
r_long_range_B_other5.112
r_scangle_other4.188
r_scbond_it2.786
r_scbond_other2.784
r_mcangle_it2.378
r_mcangle_other2.378
r_angle_refined_deg2.084
r_mcbond_it1.755
r_mcbond_other1.753
r_angle_other_deg1.309
r_chiral_restr0.132
r_bond_refined_d0.022
r_gen_planes_refined0.012
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 Atoms155
Heterogen Atoms6

Software

Software
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
Aimlessdata scaling