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Mutant Src SH2 domain in complex with phosphotyrosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4F59
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 290 VAPOR DIFFUSION,
SITTING DROP, TEMPERATURE 290K
0.2 M Ammonium Fluoride, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.16 43.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.674 α = 90 b = 67.674 β = 90 c = 46.759 γ = 120
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 16M SI 111 CRYSTAL 2023-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.97934 NSLS-II 17-ID-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.61 29.3 99.4 0.068 16.5 8.1 15693
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.61 1.66 95.3 0.54 2.1 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.61 29.3 15213 472 99.38 0.12392 0.12215 0.17569 0.2114 RANDOM 35.391
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] -0.05 -0.03 -0.05 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.66 r_dihedral_angle_4_deg 18.288 r_rigid_bond_restr 17.702 r_dihedral_angle_3_deg 15.139 r_scangle_other 12.085 r_scbond_other 12.045 r_scbond_it 12.004 r_long_range_B_refined 9.903 r_long_range_B_other 9.889 r_mcbond_it 7.612
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.66 r_dihedral_angle_4_deg 18.288 r_rigid_bond_restr 17.702 r_dihedral_angle_3_deg 15.139 r_scangle_other 12.085 r_scbond_other 12.045 r_scbond_it 12.004 r_long_range_B_refined 9.903 r_long_range_B_other 9.889 r_mcbond_it 7.612 r_mcbond_other 7.611 r_dihedral_angle_1_deg 7.468 r_mcangle_it 6.827 r_mcangle_other 6.821 r_angle_refined_deg 1.8 r_angle_other_deg 1.522 r_chiral_restr 0.081 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_gen_planes_other 0.005 r_bond_other_d 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 882 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing