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Crystal structure of PLCG1 SH2(C) domain with a triple Tyr phosphorylated peptide derived from NTRK1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EY0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.2 M NaCl, 0.1 M phosphate-citrate, pH 4.2, 20% PEG8000
Crystal Properties Matthews coefficient Solvent content 3.14 60.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.69 α = 90 b = 157.69 β = 90 c = 158.2 γ = 90
Symmetry Space Group P 41 21 2
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 EIGER X 9M 2024-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.96183 SSRF BL10U2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 70.7 100 0.9999 15.71 26.5 78013
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.55 100 0.663
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.4 70.7 1.35 78013 3902 99.91 0.2176 0.2154 0.2152 0.2591 0.2584
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.506 f_angle_d 0.541 f_chiral_restr 0.04 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10901 Nucleic Acid Atoms Solvent Atoms 351 Heterogen Atoms 53
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PHENIX phasing autoPROC data processing XDS data reduction