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Crystal structure of Sphingosine Kinase 1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 sitting drop 6 289 1.0-1.4M ammonium sulfate, 0.3-1.3M NaCl, 0.1M Bis-Tris,, pH 6.0, sitting drop, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.57 52.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.859 α = 90 b = 226.263 β = 90 c = 106.487 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC315R 3x3 CCD array SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0000 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2 113.131 99.7 0.062 13.2 4.3 82888 82888
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 98.5 0.488 0.488 1.6 3.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2 48.22 78720 4143 99.68 0.21545 0.21303 0.26185 0.2668 RANDOM 39.712
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] 0.97 -0.15 -0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.52 r_dihedral_angle_4_deg 20.139 r_dihedral_angle_3_deg 18.036 r_dihedral_angle_1_deg 6.085 r_angle_refined_deg 1.312 r_angle_other_deg 0.78 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.52 r_dihedral_angle_4_deg 20.139 r_dihedral_angle_3_deg 18.036 r_dihedral_angle_1_deg 6.085 r_angle_refined_deg 1.312 r_angle_other_deg 0.78 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it 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 8142 Nucleic Acid Atoms Solvent Atoms 384 Heterogen Atoms 117
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction