5LQ4

The Structure of ThcOx, the First Oxidase Protein from the Cyanobactin Pathways


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.752931.0 M sodium citrate, 0.1 M CHES pH 7.75
2VAPOR DIFFUSION7.752931.0 M sodium citrate, 0.1 M CHES pH 7.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.3α = 90
b = 109.3β = 90
c = 195.36γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2015-04-20MSINGLE WAVELENGTH
22x-ray50PIXELDECTRIS PILATUS 12M2016-02-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I031.7712DiamondI03
2SYNCHROTRONDIAMOND BEAMLINE I233.0955DiamondI23

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
12.6572.841000.08317.98.13520460.235
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)
12.652.7299.60.8362.78.5

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 DIFFRACTIONSADTHROUGHOUT2.6572.8333383175199.920.198150.196640.22838RANDOM74.681
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]
0.380.38-0.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.047
r_dihedral_angle_4_deg16.459
r_dihedral_angle_3_deg13.562
r_long_range_B_refined7.67
r_long_range_B_other7.67
r_dihedral_angle_1_deg6.711
r_scangle_other5.199
r_mcangle_it4.755
r_mcangle_other4.755
r_scbond_it3.218
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.047
r_dihedral_angle_4_deg16.459
r_dihedral_angle_3_deg13.562
r_long_range_B_refined7.67
r_long_range_B_other7.67
r_dihedral_angle_1_deg6.711
r_scangle_other5.199
r_mcangle_it4.755
r_mcangle_other4.755
r_scbond_it3.218
r_scbond_other3.217
r_mcbond_it2.919
r_mcbond_other2.919
r_angle_refined_deg1.294
r_angle_other_deg1.056
r_chiral_restr0.071
r_bond_refined_d0.008
r_gen_planes_refined0.005
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7344
Nucleic Acid Atoms
Solvent Atoms4
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing