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Crystal structure of Src kinase domain in complex with covalent inhibitor
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.94 58.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.099 α = 78.73 b = 63.255 β = 88.04 c = 73.799 γ = 89.95
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 210 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 ALS 8.3.1
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 2.48 43.1 96.3 31050
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 2.5 72.36 25198 1273 97.53 0.238 0.23807 0.235 0.2307 0.292 0.2804 RANDOM 29.206
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] -0.45 -0.08 -0.41 -1.22 1.28 1.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.743 r_dihedral_angle_3_deg 18.253 r_dihedral_angle_4_deg 15.065 r_dihedral_angle_1_deg 6.138 r_scangle_it 3.218 r_scbond_it 1.963 r_angle_refined_deg 1.676 r_mcangle_it 1.464 r_mcbond_it 0.857 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.743 r_dihedral_angle_3_deg 18.253 r_dihedral_angle_4_deg 15.065 r_dihedral_angle_1_deg 6.138 r_scangle_it 3.218 r_scbond_it 1.963 r_angle_refined_deg 1.676 r_mcangle_it 1.464 r_mcbond_it 0.857 r_nbtor_refined 0.314 r_symmetry_vdw_refined 0.264 r_nbd_refined 0.23 r_xyhbond_nbd_refined 0.172 r_symmetry_hbond_refined 0.122 r_chiral_restr 0.106 r_bond_refined_d 0.016 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3789 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 50
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