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The tandem SH2 domains of SYK with a bound FCER1G 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 2.37 48.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.136 α = 90 b = 88.035 β = 113.575 c = 158.486 γ = 90
Symmetry Space Group C 1 2 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 2021-01-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 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 73.26 98.3 0.145 0.164 0.077 0.995 7.5 8.3 90843
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 83.8 1.672 2.018 1.1 0.31 0.7 4.9
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 73.26 90756 1981 98.264 0.209 0.2075 0.2116 0.255 0.2584 63.047
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] -1.865 1.846 -2.006 1.636
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.606 r_dihedral_angle_4_deg 20.956 r_dihedral_angle_3_deg 16.039 r_lrange_other 12.529 r_lrange_it 12.522 r_scangle_it 9.328 r_scangle_other 9.328 r_mcangle_it 8.368 r_mcangle_other 8.368 r_dihedral_angle_1_deg 7.164
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.606 r_dihedral_angle_4_deg 20.956 r_dihedral_angle_3_deg 16.039 r_lrange_other 12.529 r_lrange_it 12.522 r_scangle_it 9.328 r_scangle_other 9.328 r_mcangle_it 8.368 r_mcangle_other 8.368 r_dihedral_angle_1_deg 7.164 r_scbond_it 6.195 r_scbond_other 6.194 r_mcbond_it 5.681 r_mcbond_other 5.681 r_angle_refined_deg 1.506 r_angle_other_deg 1.266 r_symmetry_xyhbond_nbd_refined 0.334 r_ncsr_local_group_17 0.236 r_ncsr_local_group_19 0.225 r_nbd_other 0.218 r_nbd_refined 0.211 r_ncsr_local_group_16 0.206 r_ncsr_local_group_20 0.205 r_ncsr_local_group_18 0.197 r_ncsr_local_group_21 0.197 r_symmetry_nbd_other 0.184 r_symmetry_nbd_refined 0.179 r_nbtor_refined 0.163 r_xyhbond_nbd_refined 0.159 r_ncsr_local_group_13 0.125 r_ncsr_local_group_5 0.124 r_ncsr_local_group_4 0.123 r_ncsr_local_group_3 0.122 r_ncsr_local_group_11 0.122 r_ncsr_local_group_7 0.12 r_ncsr_local_group_8 0.119 r_ncsr_local_group_10 0.119 r_ncsr_local_group_12 0.118 r_ncsr_local_group_1 0.111 r_ncsr_local_group_15 0.111 r_ncsr_local_group_9 0.11 r_ncsr_local_group_2 0.106 r_ncsr_local_group_14 0.106 r_ncsr_local_group_6 0.1 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.069 r_symmetry_xyhbond_nbd_other 0.066 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 13083 Nucleic Acid Atoms Solvent Atoms 334 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing