6CJB

Crystal structure of Cystathionine beta-lyase from Legionella pneumophila Philadelphia 1 covalently bound to Pyridoxal phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4IY7PDB entry 4iy7 teramer as per Morda

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8285Molecular Dimensions Morpheus screen G7: 10% PEG 4000, 25% Glycerol, 20mM of each N-formate, trisodium citrate, sodium potassium l-tartrate sodium oxamate: 100M MOPS/HEPES-Na pH 7.5: LepnA.00906.a.B1.PS38320 at 18.01mg/ml + 3mM PLP, 3mM Homocysteine, 3mM Pyruvate: cryo: direct: tray 295496 G7: puck MWL3-10
Crystal Properties
Matthews coefficientSolvent content
2.448.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.07α = 90
b = 97.06β = 90
c = 176.86γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2017-10-26MSINGLE 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
11.7546.899.70.0380.043123.824.86716614520.53
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)
11.751.898.30.510.630.742.12.894

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 REPLACEMENTTHROUGHOUTPDB entry 4iy7 teramer as per Morda1.7546.81.35166128199199.720.14690.14660.16927.3108
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 Atoms11630
Nucleic Acid Atoms
Solvent Atoms1328
Heterogen Atoms18

Software

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