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The tandem SH2 domains of SYK with a bound CD3G 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 6 293 100 mM MMT buffer, 30% PEG 1000
Crystal Properties Matthews coefficient Solvent content 2.91 57.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.321 α = 90 b = 129.312 β = 100.232 c = 95.346 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 EIGER2 XE 16M 2021-05-15 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 2.4 93.83 99.9 0.219 0.25 0.116 0.992 7.4 8.9 86011
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 2.4 2.44 99.5 2.507 2.849 1.317 0.395 0.9 9.3
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 2.4 93.83 85907 1977 99.878 0.218 0.2165 0.2197 0.2588 0.26 45.203
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] -1.589 -1.88 -0.554 2.649
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.958 r_dihedral_angle_4_deg 18.025 r_dihedral_angle_3_deg 16.932 r_lrange_other 9.648 r_lrange_it 9.643 r_dihedral_angle_1_deg 7.294 r_scangle_it 7.107 r_scangle_other 7.107 r_mcangle_it 6.398 r_mcangle_other 6.398
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.958 r_dihedral_angle_4_deg 18.025 r_dihedral_angle_3_deg 16.932 r_lrange_other 9.648 r_lrange_it 9.643 r_dihedral_angle_1_deg 7.294 r_scangle_it 7.107 r_scangle_other 7.107 r_mcangle_it 6.398 r_mcangle_other 6.398 r_scbond_it 4.587 r_scbond_other 4.586 r_mcbond_it 4.202 r_mcbond_other 4.201 r_angle_refined_deg 1.522 r_angle_other_deg 1.234 r_symmetry_xyhbond_nbd_refined 0.288 r_nbd_refined 0.205 r_nbd_other 0.202 r_ncsr_local_group_21 0.189 r_symmetry_nbd_other 0.18 r_xyhbond_nbd_refined 0.17 r_ncsr_local_group_27 0.166 r_nbtor_refined 0.162 r_ncsr_local_group_16 0.161 r_ncsr_local_group_26 0.151 r_ncsr_local_group_20 0.149 r_symmetry_nbd_refined 0.147 r_ncsr_local_group_29 0.147 r_ncsr_local_group_17 0.145 r_ncsr_local_group_22 0.139 r_ncsr_local_group_25 0.134 r_ncsr_local_group_23 0.132 r_ncsr_local_group_30 0.126 r_ncsr_local_group_24 0.117 r_ncsr_local_group_5 0.106 r_ncsr_local_group_1 0.103 r_symmetry_xyhbond_nbd_other 0.101 r_ncsr_local_group_8 0.101 r_ncsr_local_group_9 0.101 r_ncsr_local_group_11 0.1 r_ncsr_local_group_2 0.099 r_ncsr_local_group_15 0.099 r_ncsr_local_group_12 0.097 r_ncsr_local_group_19 0.096 r_ncsr_local_group_7 0.095 r_ncsr_local_group_13 0.095 r_ncsr_local_group_3 0.093 r_ncsr_local_group_10 0.093 r_ncsr_local_group_28 0.086 r_ncsr_local_group_14 0.083 r_ncsr_local_group_18 0.082 r_symmetry_nbtor_other 0.075 r_ncsr_local_group_4 0.074 r_chiral_restr 0.067 r_ncsr_local_group_6 0.063 r_bond_refined_d 0.009 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 13363 Nucleic Acid Atoms Solvent Atoms 613 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing