8AYF

Crystal structure of human Sphingosine-1-phosphate lyase 1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5294Protein solution: hSPL 108uM in Tris-HCl 20 mM pH 8.0 NaCl 150 mM DTT 1mM Glycerol 5% Precipitant: (Hit G4 of Molecular Dimension screen Morpheus) 0.02M Sodium formate; 0.02M Ammonium acetate; 0.02M Sodium citrate tribasic dihydrate; 0.02M Potassium sodium tartrate tetrahydrate; 0.02M Sodium oxamate; Imidazole 0.05M; MES monohydrate (acid) 0.05M; 12.5% v/v MPD; 12.5% PEG 1000; 12.5% w/v PEG 3350 mixing volumes: 0.3 + 0.3 uL
Crystal Properties
Matthews coefficientSolvent content
1.9737.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.16α = 90
b = 127.41β = 104.85
c = 66.95γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MCilindrical Mirror with 50 nm Pt-coating Radius (calculated) = 14 km Distance from source = 21200 mm Incidence angle = 3 mrad Active length = 1200 mm2022-02-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 5.2R1.0000ELETTRA5.2R

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.8457.7692.60.997.86.24760418.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.842.0967.40.4211.76.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4Q6R1.8457.7645105249957.270.1920.19070.2145RANDOM21.609
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]
-0.110.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.486
r_dihedral_angle_1_deg6.44
r_dihedral_angle_2_deg5.549
r_angle_refined_deg1.408
r_angle_other_deg0.518
r_chiral_restr0.066
r_bond_other_d0.011
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6858
Nucleic Acid Atoms
Solvent Atoms319
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction