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Crystal structure of Src kinase domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other active Src kinase domain in complex with CGP77675
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 297 20% ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.93 58.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.867 α = 100.52 b = 62.542 β = 88.88 c = 73.902 γ = 89.99
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH 2003-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00075 SLS X06SA
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 1.95 20 93.9 0.135 6.8 51365
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.95 2.2 90.4 0.334 3.7
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT active Src kinase domain in complex with CGP77675 1.95 20 48107 2542 94.33 0.2162 0.21403 0.25811 RANDOM 27.65
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] -0.93 -0.07 -0.11 -1.7 0.11 2.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.384 r_dihedral_angle_4_deg 18.866 r_dihedral_angle_3_deg 15.907 r_dihedral_angle_1_deg 6.029 r_scangle_it 3.878 r_scbond_it 2.533 r_mcangle_it 1.672 r_angle_refined_deg 1.496 r_mcbond_it 1.054 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.384 r_dihedral_angle_4_deg 18.866 r_dihedral_angle_3_deg 15.907 r_dihedral_angle_1_deg 6.029 r_scangle_it 3.878 r_scbond_it 2.533 r_mcangle_it 1.672 r_angle_refined_deg 1.496 r_mcbond_it 1.054 r_nbtor_refined 0.305 r_nbd_refined 0.209 r_symmetry_hbond_refined 0.208 r_symmetry_vdw_refined 0.198 r_xyhbond_nbd_refined 0.184 r_chiral_restr 0.099 r_bond_refined_d 0.016 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3622 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling AMoRE phasing