8K5K

The structure of SenA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4X8B 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP829120% PEG 6000, 0.1 M Tris/HCl pH 8.0, 0.2 M ammonium chloride
Crystal Properties
Matthews coefficientSolvent content
2.1743.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.711α = 90
b = 95.841β = 90
c = 62.147γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELBruker PHOTON III2023-04-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1LIQUID ANODEBRUKER METALJET1.34138

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
11.8134.3899.40.069615.337.0837959
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)
11.811.8496.60.44392.114.47

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 REPLACEMENTTHROUGHOUT1.8134.3835938187299.150.173610.170780.22866RANDOM24.134
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]
-0.871.01-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.635
r_dihedral_angle_4_deg17.02
r_dihedral_angle_3_deg14.691
r_dihedral_angle_1_deg7.167
r_long_range_B_refined5.748
r_long_range_B_other5.532
r_scangle_other3.69
r_mcangle_it2.889
r_mcangle_other2.888
r_scbond_it2.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.635
r_dihedral_angle_4_deg17.02
r_dihedral_angle_3_deg14.691
r_dihedral_angle_1_deg7.167
r_long_range_B_refined5.748
r_long_range_B_other5.532
r_scangle_other3.69
r_mcangle_it2.889
r_mcangle_other2.888
r_scbond_it2.45
r_scbond_other2.45
r_mcbond_it2.069
r_mcbond_other2.069
r_angle_refined_deg1.578
r_angle_other_deg1.421
r_chiral_restr0.084
r_bond_refined_d0.01
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 Atoms3137
Nucleic Acid Atoms
Solvent Atoms492
Heterogen Atoms19

Software

Software
Software NamePurpose
SAINTdata reduction
SAINTdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing