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Crystal structure of human Sphingosine-1-phosphate lyase 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Q6R 4Q6R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 294 Protein 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 coefficient Solvent content 1.97 37.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.16 α = 90 b = 127.41 β = 104.85 c = 66.95 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M Cilindrical Mirror with 50 nm Pt-coating Radius (calculated) = 14 km Distance from source = 21200 mm Incidence angle = 3 mrad Active length = 1200 mm 2022-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.0000 ELETTRA 5.2R
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.84 57.76 92.6 0.99 7.8 6.2 47604 18.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.84 2.09 67.4 0.421 1.7 6.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4Q6R 1.84 57.76 45105 2499 57.27 0.192 0.1907 0.1982 0.2145 0.2202 RANDOM 21.609
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] -0.11 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.486 r_dihedral_angle_1_deg 6.44 r_dihedral_angle_2_deg 5.549 r_angle_refined_deg 1.408 r_angle_other_deg 0.518 r_chiral_restr 0.066 r_bond_other_d 0.011 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6858 Nucleic Acid Atoms Solvent Atoms 319 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing PDB_EXTRACT data extraction