7Q5W

The tandem SH2 domains of SYK with a bound TYROBP diphospho-ITAM peptide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529330 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 coefficientSolvent content
2.9358.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.949α = 90
b = 131.928β = 90
c = 141.526γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2021-06-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.265.961000.1320.1370.0390.9991424.2112454
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)RedundancyNumber Unique Reflections (All)
12.22.241004.1914.2591.1950.5710.825.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1A812.265.96112358201899.9860.2340.23360.266361.064
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]
1.15-3.2882.138
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.027
r_dihedral_angle_4_deg19.833
r_dihedral_angle_3_deg16.967
r_lrange_other10.661
r_lrange_it10.655
r_scangle_it7.933
r_scangle_other7.933
r_mcangle_it7.577
r_mcangle_other7.577
r_dihedral_angle_1_deg7.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.027
r_dihedral_angle_4_deg19.833
r_dihedral_angle_3_deg16.967
r_lrange_other10.661
r_lrange_it10.655
r_scangle_it7.933
r_scangle_other7.933
r_mcangle_it7.577
r_mcangle_other7.577
r_dihedral_angle_1_deg7.09
r_scbond_it5.154
r_scbond_other5.154
r_mcbond_it5.076
r_mcbond_other5.074
r_angle_refined_deg1.42
r_angle_other_deg1.207
r_nbd_other0.213
r_nbd_refined0.203
r_ncsr_local_group_290.197
r_ncsr_local_group_230.192
r_symmetry_nbd_other0.173
r_xyhbond_nbd_refined0.17
r_ncsr_local_group_240.164
r_nbtor_refined0.161
r_ncsr_local_group_210.161
r_ncsr_local_group_260.159
r_ncsr_local_group_280.159
r_symmetry_xyhbond_nbd_refined0.149
r_ncsr_local_group_200.147
r_ncsr_local_group_180.14
r_ncsr_local_group_160.136
r_ncsr_local_group_220.136
r_symmetry_nbd_refined0.133
r_ncsr_local_group_250.13
r_ncsr_local_group_270.129
r_symmetry_xyhbond_nbd_other0.126
r_ncsr_local_group_300.123
r_ncsr_local_group_190.117
r_ncsr_local_group_170.106
r_ncsr_local_group_40.098
r_ncsr_local_group_120.098
r_ncsr_local_group_140.097
r_ncsr_local_group_130.095
r_ncsr_local_group_70.094
r_ncsr_local_group_80.094
r_ncsr_local_group_110.094
r_ncsr_local_group_90.091
r_ncsr_local_group_150.091
r_ncsr_local_group_20.09
r_ncsr_local_group_50.09
r_ncsr_local_group_60.088
r_ncsr_local_group_30.085
r_ncsr_local_group_10.084
r_symmetry_nbtor_other0.074
r_ncsr_local_group_100.071
r_chiral_restr0.061
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13148
Nucleic Acid Atoms
Solvent Atoms303
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing