5FGS

Crystal structure of C-terminal domain of shaft pilin spaA from Lactobacillus rhamnosus GG - P21212 space group


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52950.1M MES, 0.02M zinc sulphate, 25% PEG 550MME
Crystal Properties
Matthews coefficientSolvent content
2.2841.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.07α = 90
b = 74.343β = 90
c = 116.777γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2014-03-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEXenocs GeniX 3D Cu HF1.54179

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
1237.1799.30.06324.29.233984
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)
122.11970.6492.98.8

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 REPLACEMENTTHROUGHOUT5FGR237.1732254169799.150.218160.216540.2497RANDOM43.744
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]
0.411.6-2.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.756
r_dihedral_angle_4_deg15.232
r_dihedral_angle_3_deg11.869
r_long_range_B_refined6.453
r_long_range_B_other6.395
r_dihedral_angle_1_deg6.381
r_scangle_other1.471
r_mcangle_it1.395
r_mcangle_other1.395
r_angle_refined_deg1.165
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.756
r_dihedral_angle_4_deg15.232
r_dihedral_angle_3_deg11.869
r_long_range_B_refined6.453
r_long_range_B_other6.395
r_dihedral_angle_1_deg6.381
r_scangle_other1.471
r_mcangle_it1.395
r_mcangle_other1.395
r_angle_refined_deg1.165
r_angle_other_deg1.019
r_scbond_it0.922
r_scbond_other0.922
r_mcbond_it0.855
r_mcbond_other0.855
r_chiral_restr0.061
r_bond_refined_d0.008
r_bond_other_d0.005
r_gen_planes_refined0.005
r_gen_planes_other0.004
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 Atoms3728
Nucleic Acid Atoms
Solvent Atoms256
Heterogen Atoms9

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata processing
Aimlessdata scaling
PHASERphasing
Cootmodel building