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The Crystal Structure of SYK from Biortus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XBB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M Li2SO4, 0.1M Bis-Tris pH6.5, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.92 36.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.095 α = 90 b = 83.903 β = 101.519 c = 39.962 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 X 9M 2023-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.95373 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.8 41.951 99.9 0.069 12.8 5.7 22844
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 0.763
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 1.8 41.951 22820 1118 99.886 0.192 0.1894 0.1993 0.244 0.2494 32.56
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] 2.903 -1.396 -1.725 -0.562
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.749 r_dihedral_angle_4_deg 16.209 r_dihedral_angle_3_deg 13.759 r_dihedral_angle_1_deg 6.09 r_lrange_it 5.222 r_lrange_other 5.197 r_scangle_it 3.558 r_scangle_other 3.557 r_mcangle_it 2.901 r_mcangle_other 2.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.749 r_dihedral_angle_4_deg 16.209 r_dihedral_angle_3_deg 13.759 r_dihedral_angle_1_deg 6.09 r_lrange_it 5.222 r_lrange_other 5.197 r_scangle_it 3.558 r_scangle_other 3.557 r_mcangle_it 2.901 r_mcangle_other 2.9 r_scbond_it 2.213 r_scbond_other 2.212 r_mcbond_it 1.889 r_mcbond_other 1.889 r_angle_refined_deg 1.274 r_angle_other_deg 1.217 r_symmetry_xyhbond_nbd_refined 0.202 r_nbd_refined 0.189 r_symmetry_nbd_other 0.166 r_nbtor_refined 0.165 r_nbd_other 0.163 r_xyhbond_nbd_refined 0.158 r_symmetry_nbd_refined 0.122 r_symmetry_nbtor_other 0.072 r_chiral_restr 0.058 r_symmetry_xyhbond_nbd_other 0.043 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2144 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing