3NNG

Crystal structure of the F5/8 type C domain of Q5LFR2_BACFN protein from Bacteroides fragilis. Northeast Structural Genomics Consortium Target BfR258E


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1K3IPDB entry 1k3i

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1Microbatch under Paraffin oil729140% PEG 4000, 0.1M calcium chloride, 0.1M Bis-Tris Propane, pH 7.0, Microbatch under Paraffin oil, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
1.6826.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.208α = 90
b = 62.463β = 90
c = 72.001γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2009-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4C0.97907NSLSX4C

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
12.1775099.90.08821.84.3260922606625.6
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)
2.182.261000.2155.73.92589

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1k3i2.17731.2320.8526014129699.640.1670.1640.224RANDOM28.961
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]
6.1761.281-7.457
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d18.528
f_angle_d1.026
f_chiral_restr0.074
f_bond_d0.007
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2418
Nucleic Acid Atoms
Solvent Atoms109
Heterogen Atoms2

Software

Software
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
Rosettaphasing
CNSphasing
PHENIXphasing