3EUR

Crystal structure of the C-terminal domain of uncharacterized protein from Bacteroides fragilis NCTC 9343


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52770.2 M Potassium sodium tartrate tetrahydrate 20% Peg 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.1943.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 33.145α = 90
b = 43.428β = 90
c = 98.692γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDSBC-3mirror2008-09-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.9794APS19-BM

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
11.35091.20.04344.78356473276322
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)
11.31.334500.155.144884

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.349.33223267531061164691.090.140320.140320.138720.17009RANDOM12.084
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]
0.170.29-0.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.543
r_dihedral_angle_4_deg14.41
r_dihedral_angle_3_deg12.804
r_sphericity_free10.178
r_dihedral_angle_1_deg6.242
r_scangle_it5.331
r_sphericity_bonded4.678
r_scbond_it3.709
r_mcangle_it2.858
r_mcbond_it1.856
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.543
r_dihedral_angle_4_deg14.41
r_dihedral_angle_3_deg12.804
r_sphericity_free10.178
r_dihedral_angle_1_deg6.242
r_scangle_it5.331
r_sphericity_bonded4.678
r_scbond_it3.709
r_mcangle_it2.858
r_mcbond_it1.856
r_angle_refined_deg1.711
r_rigid_bond_restr1.65
r_angle_other_deg1.019
r_mcbond_other0.869
r_chiral_restr0.12
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_bond_other_d0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1128
Nucleic Acid Atoms
Solvent Atoms230
Heterogen Atoms

Software

Software
Software NamePurpose
SBC-Collectdata collection
HKL-3000phasing
SHELXmodel building
Cootmodel building
MLPHAREphasing
PHENIXmodel building
REFMACrefinement
ARP/wARPmodel building
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
PHENIXphasing
REFMACphasing