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Crystal structure of Sphingosine Kinase 1 with inhibitor and ADP
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 52.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.202 α = 90 b = 106.573 β = 90 c = 226.02 γ = 90
Symmetry Space Group P 21 21 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 MAD
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 Merge I (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 2.3 113.228 98.8 0.065 0.065 14.3 3.6 108742 108742
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.42 97.3 0.368 0.368 0.432 0.223 2 3.5 15455
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 MAD THROUGHOUT 2.3 50 108661 5435 98.61 0.2086 0.2055 0.2055 0.2686 0.268 RANDOM 38.7938
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] 1.18 -0.99 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.549 r_dihedral_angle_4_deg 22.322 r_dihedral_angle_3_deg 21.358 r_dihedral_angle_1_deg 7.459 r_scangle_it 4.74 r_scbond_it 2.998 r_angle_refined_deg 2.04 r_mcangle_it 2.024 r_mcbond_it 1.099 r_chiral_restr 0.148
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.549 r_dihedral_angle_4_deg 22.322 r_dihedral_angle_3_deg 21.358 r_dihedral_angle_1_deg 7.459 r_scangle_it 4.74 r_scbond_it 2.998 r_angle_refined_deg 2.04 r_mcangle_it 2.024 r_mcbond_it 1.099 r_chiral_restr 0.148 r_bond_refined_d 0.02 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16208 Nucleic Acid Atoms Solvent Atoms 358 Heterogen Atoms 209
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction