5LQ1

1.41 A resolution structure of PtxB from Trichodesmium erythraeum IMS101 in complex with methylphosphonate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5JVB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP52900.2 M Magnesium chloride, 0.1 M Sodium acetate pH 5.0 and 20 % (w/v) PEG 6000
Crystal Properties
Matthews coefficientSolvent content
2.1542.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.481α = 84.82
b = 53.703β = 78.26
c = 66.388γ = 69.74
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-07-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97629DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.4165.0595.20.0320.9999.13.391920
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.411.4375.40.6640.481.12.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT5JVB1.4164.9886075435093.660.182210.17980.23031RANDOM26.361
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]
0.920.69-0.290.15-0.18-0.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.506
r_sphericity_bonded31.373
r_sphericity_free20.522
r_dihedral_angle_4_deg18.193
r_dihedral_angle_3_deg12.98
r_scbond_it9.544
r_scbond_other9.544
r_rigid_bond_restr8.723
r_scangle_other8.096
r_long_range_B_refined6.458
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.506
r_sphericity_bonded31.373
r_sphericity_free20.522
r_dihedral_angle_4_deg18.193
r_dihedral_angle_3_deg12.98
r_scbond_it9.544
r_scbond_other9.544
r_rigid_bond_restr8.723
r_scangle_other8.096
r_long_range_B_refined6.458
r_long_range_B_other6.458
r_dihedral_angle_1_deg5.876
r_mcangle_other4.089
r_mcangle_it4.088
r_mcbond_it3.891
r_mcbond_other3.891
r_angle_refined_deg1.514
r_angle_other_deg1.109
r_chiral_restr0.091
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.002
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 Atoms3998
Nucleic Acid Atoms
Solvent Atoms213
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing