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Structure of sphingosine-1-phosphate lyase (SPL) from Aspergillus fumigatus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8AYF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 294 0.1M Hepes sodium pH 7.5
1.4 M Sodium citrate tribasic dihydrate
DMSO 1%
Cryoprotection = mother liquor + 20% Glycerol
AfuSPL = 93 microM
Crystal Properties Matthews coefficient Solvent content 2.63 53.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.07 α = 90 b = 130.07 β = 90 c = 234.06 γ = 120
Symmetry Space Group P 65 2 2
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 2022-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.0000 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.46 101.5 95.1 0.317 0.998 15.1 36.7 12600
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 3.46 3.74 71.9 0.572 1.5 39
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3.46 100.02 11394 1205 79 0.28465 0.28351 0.2836 0.29551 0.2964 RANDOM 121.81
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] -0.19 -0.1 -0.19 0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 13.556 r_dihedral_angle_3_deg 12 r_long_range_B_refined 10.65 r_long_range_B_other 10.65 r_scangle_other 6.494 r_mcangle_it 6.179 r_mcangle_other 6.178 r_dihedral_angle_1_deg 5.409 r_scbond_it 3.758 r_scbond_other 3.757
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 13.556 r_dihedral_angle_3_deg 12 r_long_range_B_refined 10.65 r_long_range_B_other 10.65 r_scangle_other 6.494 r_mcangle_it 6.179 r_mcangle_other 6.178 r_dihedral_angle_1_deg 5.409 r_scbond_it 3.758 r_scbond_other 3.757 r_mcbond_it 3.591 r_mcbond_other 3.588 r_angle_refined_deg 0.89 r_angle_other_deg 0.308 r_chiral_restr 0.041 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7343 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction MOLREP phasing