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The tandem SH2 domains of SYK with a bound TYROBP diphospho-ITAM peptide
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 8.5 293 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulphate, 100 mM Tris/BICINE, 10% PEG 20,000, 20% PEG 500 MME
Crystal Properties Matthews coefficient Solvent content 2.93 58.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.949 α = 90 b = 131.928 β = 90 c = 141.526 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 PIXEL DECTRIS EIGER2 XE 16M 2021-06-27 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 2.2 65.96 100 0.132 0.137 0.039 0.999 14 24.2 112454
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 2.2 2.24 100 4.191 4.259 1.195 0.571 0.8 25.8
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 2.2 65.96 112358 2018 99.986 0.234 0.2336 0.2374 0.2663 0.2666 61.064
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] 1.15 -3.288 2.138
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.027 r_dihedral_angle_4_deg 19.833 r_dihedral_angle_3_deg 16.967 r_lrange_other 10.661 r_lrange_it 10.655 r_scangle_it 7.933 r_scangle_other 7.933 r_mcangle_it 7.577 r_mcangle_other 7.577 r_dihedral_angle_1_deg 7.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.027 r_dihedral_angle_4_deg 19.833 r_dihedral_angle_3_deg 16.967 r_lrange_other 10.661 r_lrange_it 10.655 r_scangle_it 7.933 r_scangle_other 7.933 r_mcangle_it 7.577 r_mcangle_other 7.577 r_dihedral_angle_1_deg 7.09 r_scbond_it 5.154 r_scbond_other 5.154 r_mcbond_it 5.076 r_mcbond_other 5.074 r_angle_refined_deg 1.42 r_angle_other_deg 1.207 r_nbd_other 0.213 r_nbd_refined 0.203 r_ncsr_local_group_29 0.197 r_ncsr_local_group_23 0.192 r_symmetry_nbd_other 0.173 r_xyhbond_nbd_refined 0.17 r_ncsr_local_group_24 0.164 r_nbtor_refined 0.161 r_ncsr_local_group_21 0.161 r_ncsr_local_group_26 0.159 r_ncsr_local_group_28 0.159 r_symmetry_xyhbond_nbd_refined 0.149 r_ncsr_local_group_20 0.147 r_ncsr_local_group_18 0.14 r_ncsr_local_group_16 0.136 r_ncsr_local_group_22 0.136 r_symmetry_nbd_refined 0.133 r_ncsr_local_group_25 0.13 r_ncsr_local_group_27 0.129 r_symmetry_xyhbond_nbd_other 0.126 r_ncsr_local_group_30 0.123 r_ncsr_local_group_19 0.117 r_ncsr_local_group_17 0.106 r_ncsr_local_group_4 0.098 r_ncsr_local_group_12 0.098 r_ncsr_local_group_14 0.097 r_ncsr_local_group_13 0.095 r_ncsr_local_group_7 0.094 r_ncsr_local_group_8 0.094 r_ncsr_local_group_11 0.094 r_ncsr_local_group_9 0.091 r_ncsr_local_group_15 0.091 r_ncsr_local_group_2 0.09 r_ncsr_local_group_5 0.09 r_ncsr_local_group_6 0.088 r_ncsr_local_group_3 0.085 r_ncsr_local_group_1 0.084 r_symmetry_nbtor_other 0.074 r_ncsr_local_group_10 0.071 r_chiral_restr 0.061 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13148 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing