5O37

Pseudomonas stutzeri PtxB in complex with methylphosphonate (MPn) to 1.37 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP42900.1 M MMT buffer pH 4 and 25 % (w/v) PEG 1500
Crystal Properties
Matthews coefficientSolvent content
2.3246.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.8α = 90
b = 39.12β = 90
c = 63.38γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-02-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92819DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)CC (Half)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
11.3737.6199.90.022116.811.259851
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.371.3998.80.6150.4851.27.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.3737.6156823297499.830.138930.136950.17723RANDOM22.115
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]
-0.55-0.721.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.281
r_sphericity_free25.299
r_sphericity_bonded22.969
r_dihedral_angle_4_deg13.406
r_dihedral_angle_3_deg11.535
r_rigid_bond_restr10.684
r_scbond_it8.323
r_scbond_other8.319
r_scangle_other6.731
r_dihedral_angle_1_deg5.631
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.281
r_sphericity_free25.299
r_sphericity_bonded22.969
r_dihedral_angle_4_deg13.406
r_dihedral_angle_3_deg11.535
r_rigid_bond_restr10.684
r_scbond_it8.323
r_scbond_other8.319
r_scangle_other6.731
r_dihedral_angle_1_deg5.631
r_long_range_B_refined5.58
r_long_range_B_other5.475
r_mcbond_other3.627
r_mcangle_other3.593
r_mcangle_it2.832
r_mcbond_it2.498
r_angle_refined_deg1.5
r_angle_other_deg1.494
r_chiral_restr0.093
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.003
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2016
Nucleic Acid Atoms
Solvent Atoms225
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing