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Crystal structure of SYK kinase in complex with compound 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other in-house SYK structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 277 20% PEG 3350, 0.1 M bis tris propane pH 6.5, 0.2 M Na formate
Crystal Properties Matthews coefficient Solvent content 2.09 41.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.085 α = 90 b = 84.859 β = 99.329 c = 40.845 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 EIGER R 4M CRL 2018-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.75 42.43 98.6 0.025 0.034 0.025 0.999 17.7 2 26808
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 99.4 0.32 0.453 0.32 0.881 2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.75 39.586 26808 1339 98.562 0.182 0.1802 0.1737 0.2145 0.2086 27.308
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] -1.573 -0.698 -1.559 3.189
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.902 r_dihedral_angle_6_deg 16.684 r_dihedral_angle_2_deg 13.595 r_lrange_it 7.439 r_lrange_other 7.42 r_dihedral_angle_1_deg 6.589 r_scangle_it 6.208 r_scangle_other 6.206 r_scbond_it 4.054 r_scbond_other 4.052
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.902 r_dihedral_angle_6_deg 16.684 r_dihedral_angle_2_deg 13.595 r_lrange_it 7.439 r_lrange_other 7.42 r_dihedral_angle_1_deg 6.589 r_scangle_it 6.208 r_scangle_other 6.206 r_scbond_it 4.054 r_scbond_other 4.052 r_mcangle_it 3.652 r_mcangle_other 3.651 r_mcbond_it 2.664 r_mcbond_other 2.655 r_angle_refined_deg 1.77 r_chiral_restr_other 0.819 r_angle_other_deg 0.777 r_symmetry_nbd_refined 0.373 r_nbd_other 0.286 r_nbd_refined 0.274 r_xyhbond_nbd_refined 0.215 r_symmetry_nbd_other 0.213 r_symmetry_xyhbond_nbd_refined 0.188 r_nbtor_refined 0.185 r_chiral_restr 0.093 r_symmetry_nbtor_other 0.085 r_bond_refined_d 0.011 r_symmetry_xyhbond_nbd_other 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2138 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing