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Crystal structure of human SYK in complex with compound 24
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 2.08 41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.204 α = 90 b = 87.344 β = 92.159 c = 40.048 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-F Toroidal mirror 2017-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9796 ESRF ID23-1
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 1.6 43.67 98.7 0.019 1 17.4 2 34990
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 91.9 0.318 0.823 2.2 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 1.6 43.67 34990 1746 98.513 0.178 0.1766 0.1764 0.2107 0.2107 25.887
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] 0.011 1.279 -1.001 0.891
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.455 r_dihedral_angle_3_deg 16.466 r_dihedral_angle_2_deg 12.217 r_lrange_it 7.36 r_lrange_other 7.36 r_dihedral_angle_1_deg 6.297 r_scangle_it 5.814 r_scangle_other 5.812 r_scbond_it 3.863 r_scbond_other 3.862
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.455 r_dihedral_angle_3_deg 16.466 r_dihedral_angle_2_deg 12.217 r_lrange_it 7.36 r_lrange_other 7.36 r_dihedral_angle_1_deg 6.297 r_scangle_it 5.814 r_scangle_other 5.812 r_scbond_it 3.863 r_scbond_other 3.862 r_mcangle_it 3.156 r_mcangle_other 3.155 r_mcbond_it 2.348 r_mcbond_other 2.339 r_angle_refined_deg 1.748 r_chiral_restr_other 0.849 r_angle_other_deg 0.619 r_nbd_refined 0.222 r_nbd_other 0.195 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.188 r_xyhbond_nbd_refined 0.165 r_symmetry_xyhbond_nbd_refined 0.137 r_symmetry_nbd_refined 0.127 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_symmetry_xyhbond_nbd_other 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2143 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing