☰ Navigation Tabs
Crystal Structure of Gallus gallus c-Src Kinase Domain with Point mutation Y416D and Deletion of Residues N414, T417, and R419 Bound to AMP-PNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.5 283 19% PEG 3350, 5% glycerol, 0.1 M Bis-Tris pH 5.5, and 0.2 M sodium acetate
Cryoprotectant: 30% PEG 400, 19% PEG 3350, 5% glycerol, 0.1 M Bis-Tris pH 5.5, and 0.2 M sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.13 42.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.457 α = 90 b = 62.874 β = 90 c = 105.378 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS 6M 2024-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.00 SPring-8 BL45XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.78 41.46 99.8 0.084 0.089 0.999 19.52 8.13 27180
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.78 1.89 0.731 0.779 0.852 2.79 8.35
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 AlphaFold 1.78 40.416 27180 1348 99.776 0.202 0.2001 0.21 0.2413 0.249 32.111
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] 0.159 -0.132 -0.027
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.504 r_dihedral_angle_3_deg 11.596 r_dihedral_angle_2_deg 8.05 r_lrange_it 7.749 r_lrange_other 7.738 r_dihedral_angle_1_deg 6.749 r_scangle_it 5.937 r_scangle_other 5.935 r_mcangle_it 4.455 r_mcangle_other 4.454
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.504 r_dihedral_angle_3_deg 11.596 r_dihedral_angle_2_deg 8.05 r_lrange_it 7.749 r_lrange_other 7.738 r_dihedral_angle_1_deg 6.749 r_scangle_it 5.937 r_scangle_other 5.935 r_mcangle_it 4.455 r_mcangle_other 4.454 r_scbond_it 3.997 r_scbond_other 3.997 r_mcbond_it 3.23 r_mcbond_other 3.23 r_angle_refined_deg 1.723 r_angle_other_deg 0.574 r_symmetry_nbd_refined 0.32 r_nbd_refined 0.224 r_nbtor_refined 0.188 r_nbd_other 0.188 r_symmetry_nbd_other 0.185 r_symmetry_xyhbond_nbd_refined 0.146 r_xyhbond_nbd_refined 0.13 r_chiral_restr_other 0.086 r_chiral_restr 0.084 r_symmetry_nbtor_other 0.084 r_metal_ion_refined 0.056 r_dihedral_angle_other_2_deg 0.024 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1925 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 32
Software Software Software Name Purpose XDS data scaling XDS data reduction MOLREP phasing REFMAC refinement