6YUQ

Capsule O-acetyltransferase of Neisseria meningitidis serogroup A in complex with polysaccharide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6YUO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP291.15Native wild type CsaC crystallized in sitting drop setups at concentrations of approx. 18mg/ml. Fine screens around initial screening conditions resulted in many isomorphous crystals. Mother liquor contained 50mM HEPES pH 7.0, 100 mM HEPES pH 7.6, 100mM NaCl, 5mM MgCl2, 1mM EDTA, and 31-42% PEG200. Good quality crystals grew at 4, 12, and 18C.
Crystal Properties
Matthews coefficientSolvent content
2.8356.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 137.483α = 90
b = 137.483β = 90
c = 70.253γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2017-09-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)0.97625PETRA III, EMBL c/o DESYP14 (MX2)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.9548.6299.90.0590.060.0120.99925.126.249502
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.952.0299.92.8182.8740.5650.7741.225.6

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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6YUO1.9546.271.3449462247599.870.210.20950.220771.33
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d18.6573
f_angle_d0.7536
f_chiral_restr0.0523
f_bond_d0.0056
f_plane_restr0.0036
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3898
Nucleic Acid Atoms
Solvent Atoms47
Heterogen Atoms92

Software

Software
Software NamePurpose
PHENIXrefinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
PHENIXmodel building
PHASERphasing