4POI

Crystal structure of a putative periplasmic protein (BACCAC_02096) from Bacteroides caccae ATCC 43185 at 2.30 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP27726.0% polyethylene glycol 3350, 0.20M potassium thiocyanate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.6353.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.881α = 90
b = 104.881β = 90
c = 56.07γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MFlat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)2013-11-26MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.91837,0.97895SSRLBL11-1

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
12.346.90499.70.03738.158.5614400-346.34
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)
12.32.3899.90.2757.448.8

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 DIFFRACTIONMADTHROUGHOUT2.346.9041437672299.80.24530.24360.2788RANDOM48.7819
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]
-0.99-0.991.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.739
r_dihedral_angle_3_deg14.382
r_dihedral_angle_4_deg14.048
r_dihedral_angle_1_deg5.074
r_mcangle_it3.049
r_mcbond_it1.923
r_mcbond_other1.92
r_angle_refined_deg1.502
r_angle_other_deg1.071
r_chiral_restr0.086
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.739
r_dihedral_angle_3_deg14.382
r_dihedral_angle_4_deg14.048
r_dihedral_angle_1_deg5.074
r_mcangle_it3.049
r_mcbond_it1.923
r_mcbond_other1.92
r_angle_refined_deg1.502
r_angle_other_deg1.071
r_chiral_restr0.086
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.004
r_gen_planes_other0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1878
Nucleic Acid Atoms
Solvent Atoms102
Heterogen Atoms

Software

Software
Software NamePurpose
MolProbitymodel building
PDB_EXTRACTdata extraction
SHELXphasing
SHARPphasing
XSCALEdata scaling
REFMACrefinement
XDSdata reduction
SHELXDphasing