5BPG

Crystal structure of the water-soluble FraC purified starting from the trans-membrane pore


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5293Microseeds generated in: 24% PEG 4000, 200 mM ammonium sulfate, 100 mM Cacodylate (pH 7.4) Single crystals generated in: 8% PEG 4000, 100 mM TRIS-HCl
Crystal Properties
Matthews coefficientSolvent content
2.4850.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.3α = 90
b = 44.44β = 92.82
c = 114.95γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152014-11-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.000Photon FactoryBL-5A

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
12.1447.1997.50.0999.74.542232
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)
12.142.2189.30.313.43.8

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 REPLACEMENTTHROUGHOUT3VWI2.1447.1940061211897.130.212690.210.26286RANDOM18.627
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]
-1.340.220.121.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.006
r_dihedral_angle_3_deg14.521
r_dihedral_angle_4_deg13.69
r_dihedral_angle_1_deg7.306
r_long_range_B_refined2.887
r_long_range_B_other2.771
r_angle_refined_deg1.475
r_scangle_other0.852
r_angle_other_deg0.748
r_mcangle_it0.642
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.006
r_dihedral_angle_3_deg14.521
r_dihedral_angle_4_deg13.69
r_dihedral_angle_1_deg7.306
r_long_range_B_refined2.887
r_long_range_B_other2.771
r_angle_refined_deg1.475
r_scangle_other0.852
r_angle_other_deg0.748
r_mcangle_it0.642
r_mcangle_other0.642
r_scbond_it0.533
r_scbond_other0.532
r_mcbond_it0.381
r_mcbond_other0.38
r_chiral_restr0.085
r_bond_refined_d0.012
r_gen_planes_refined0.006
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 Atoms5536
Nucleic Acid Atoms
Solvent Atoms302
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
Aimlessphasing