6CJA

Crystal structure of Cystathionine beta-lyase from Legionella pneumophila Philadelphia 1 in complex with Alanyl-PLP and Serine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherLLP bound structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8285Molecular Dimensions Morpheus screen H11: 10% w/v PEG 4000, 20% v/v glycerol: 20mM of each sodium L-glutamate, DL-alanine, glycine, DL-lysine HCl, DL-serine: 100mM bicine/Trizma base pH 8.5: LepnA.00906.a.B1.PS38320 at 18.01mg/ml: cryo: direct: tray 295502 H11: puck MWL3-7
Crystal Properties
Matthews coefficientSolvent content
2.3948.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.17α = 90
b = 97.11β = 90
c = 175.82γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2017-10-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
11.746.80399.90.0730.0770.99918.169.08618070616.39
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7499.20.4970.5690.7892.314.272

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 REPLACEMENTTHROUGHOUTLLP bound structure1.746.8031.35180685200899.920.1410.14070.16820.2527
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]
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11646
Nucleic Acid Atoms
Solvent Atoms1705
Heterogen Atoms130

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MoRDaphasing
Cootmodel building