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Crystal structure of SRC kinase domain with covalent inhibitor RL3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 16% Ethylene glycol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.97 58.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.94 α = 78.28 b = 63.53 β = 90.37 c = 74.5 γ = 89.45
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2006-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5417
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.33 72.944 90.7 0.06 0.06 11.6 3.7 32156 29166
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.33 2.46 85.9 0.407 0.407 1.8 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 2.33 72.93 32683 27702 1463 90.72 0.21508 0.2123 0.2111 0.26673 0.2618 RANDOM 32.043
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] 0.06 -0.08 0.17 -0.44 0.82 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.581 r_dihedral_angle_3_deg 17.754 r_dihedral_angle_4_deg 16.877 r_dihedral_angle_1_deg 9.703 r_scangle_it 3.433 r_scbond_it 2.237 r_angle_refined_deg 1.77 r_mcangle_it 1.642 r_mcbond_it 0.96 r_symmetry_hbond_refined 0.329
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.581 r_dihedral_angle_3_deg 17.754 r_dihedral_angle_4_deg 16.877 r_dihedral_angle_1_deg 9.703 r_scangle_it 3.433 r_scbond_it 2.237 r_angle_refined_deg 1.77 r_mcangle_it 1.642 r_mcbond_it 0.96 r_symmetry_hbond_refined 0.329 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.242 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.175 r_chiral_restr 0.124 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3892 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 93
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection MOSFLM data reduction PHASER phasing