7KZ5

Crystal structure of KabA from Bacillus cereus UW85 in complex with the plp external aldimine adduct with kanosamine-6-phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7KZ3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5291.15PEG 4000, Sodium Chloride
Crystal Properties
Matthews coefficientSolvent content
2.3547.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.67α = 77.35
b = 66.6β = 81.06
c = 111.78γ = 87.91
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2015-07-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.814CLSI08ID-1

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
11.646.74892.80.046130.062490.041860.99710.492.2227037
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)
11.61.65792.030.33870.46230.31280.7842.1

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 REPLACEMENTTHROUGHOUT7KZ31.646.7481.982270291135292.80.17680.17470.215324.7165
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_d15.093
f_angle_d1.616
f_chiral_restr0.114
f_bond_d0.02
f_plane_restr0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14148
Nucleic Acid Atoms
Solvent Atoms1204
Heterogen Atoms330

Software

Software
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
MOLREPphasing
AutoProcessdata reduction
AutoProcessdata scaling