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Crystal structure of Src kinase domain in complex with covalent inhibitor PD168393
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 323 VAPOR DIFFUSION, HANGING DROP, temperature 323K
Crystal Properties Matthews coefficient Solvent content 2.93 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.063 α = 100.74 b = 63.012 β = 89.81 c = 73.692 γ = 90.2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD ADSC QUANTUM 315 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.47 43.2 92.7 31120
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 (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.48 72.36 24586 1237 93.28 0.228 0.22768 0.225 0.2205 0.276 0.2722 RANDOM 29.821
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] 0.31 0.2 -0.13 -1.53 -1.18 0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.86 r_dihedral_angle_3_deg 17.182 r_dihedral_angle_4_deg 13.865 r_dihedral_angle_1_deg 6.08 r_mcangle_it 1.867 r_scangle_it 1.6 r_angle_refined_deg 1.435 r_mcbond_it 1.149 r_scbond_it 0.993 r_nbtor_refined 0.329
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.86 r_dihedral_angle_3_deg 17.182 r_dihedral_angle_4_deg 13.865 r_dihedral_angle_1_deg 6.08 r_mcangle_it 1.867 r_scangle_it 1.6 r_angle_refined_deg 1.435 r_mcbond_it 1.149 r_scbond_it 0.993 r_nbtor_refined 0.329 r_symmetry_vdw_refined 0.31 r_nbd_refined 0.252 r_symmetry_hbond_refined 0.225 r_xyhbond_nbd_refined 0.204 r_chiral_restr 0.094 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3687 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 46
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction AMoRE phasing