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The tandem SH2 domains of SYK
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1A81
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 200 mM, potassium thiocyanate, 12.5% glycerol, 23% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.68 54.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.902 α = 90 b = 152.58 β = 90 c = 146.824 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 PIXEL DECTRIS EIGER2 XE 16M 2021-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 1.9 146.82 100 0.166 0.173 0.043 0.998 10.7 26.4 76088
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 1.9 1.94 100 4.548 4.744 1.343 0.559 0.8 24.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 1A81 1.9 76.29 76023 1972 99.957 0.218 0.217 0.2237 0.2643 0.2679 52.278
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] -2.464 -1.151 3.615
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.717 r_dihedral_angle_4_deg 16.707 r_dihedral_angle_3_deg 15.321 r_lrange_other 9.135 r_lrange_it 9.127 r_dihedral_angle_1_deg 7.085 r_scangle_it 6.853 r_scangle_other 6.852 r_mcangle_it 5.912 r_mcangle_other 5.912
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.717 r_dihedral_angle_4_deg 16.707 r_dihedral_angle_3_deg 15.321 r_lrange_other 9.135 r_lrange_it 9.127 r_dihedral_angle_1_deg 7.085 r_scangle_it 6.853 r_scangle_other 6.852 r_mcangle_it 5.912 r_mcangle_other 5.912 r_scbond_it 4.567 r_scbond_other 4.566 r_mcbond_it 4.251 r_mcbond_other 4.222 r_angle_refined_deg 1.485 r_angle_other_deg 1.301 r_nbd_other 0.227 r_nbd_refined 0.212 r_symmetry_nbd_other 0.188 r_xyhbond_nbd_refined 0.172 r_nbtor_refined 0.163 r_symmetry_nbd_refined 0.146 r_ncsr_local_group_2 0.129 r_ncsr_local_group_3 0.127 r_ncsr_local_group_1 0.11 r_symmetry_xyhbond_nbd_refined 0.108 r_symmetry_xyhbond_nbd_other 0.105 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5928 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing