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Crystal structure of catalytic domain of the proto-oncogene tyrosine-protein kinase MER in complex with inhibitor C52
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P0C PDB ENTRY 2P0C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 287 Compound C52 (50 mM in DMSO) was added to 8 mg/ml MER protein to the final concentration of 2.5 mM. The mixture was rocked at 277 K overnight and further concentrated to about 35 mg/ml. Crystals were grown by mixing 2 microliters of MER inhibitor solution and 2 microliters of reservoir solution (100 mM Tris-HCl pH 8.5, 3.64 M NaCl) at 287 K using the hanging-drop vapor-diffusion method. Crystals were cryo-protected with a solution composed of glycerol, ethylene glycol, glucose, and fructose., VAPOR DIFFUSION, HANGING DROP, pH 8.50
Crystal Properties Matthews coefficient Solvent content 2.69 54.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.001 α = 90 b = 91.702 β = 94.06 c = 120.745 γ = 90
Symmetry Space Group P 1 21 1
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 ADSC QUANTUM 210 MIRRORS 2007-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.8 50 99 0.15 9.1 3.3 37537 -3
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) 2.8 2.9 94 0.53 2.3 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB ENTRY 2P0C 2.8 47.3 35338 35338 1889 98.73 0.275 0.27361 0.2794 0.30134 0.3077 RANDOM 42.487
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] -4.24 1.07 -4.73 9.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.029 r_dihedral_angle_3_deg 18.727 r_dihedral_angle_4_deg 17.442 r_dihedral_angle_1_deg 5.649 r_scangle_it 1.787 r_scbond_it 1.261 r_angle_refined_deg 1.239 r_mcangle_it 0.794 r_mcbond_it 0.49 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.029 r_dihedral_angle_3_deg 18.727 r_dihedral_angle_4_deg 17.442 r_dihedral_angle_1_deg 5.649 r_scangle_it 1.787 r_scbond_it 1.261 r_angle_refined_deg 1.239 r_mcangle_it 0.794 r_mcbond_it 0.49 r_nbtor_refined 0.305 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.144 r_symmetry_vdw_refined 0.139 r_symmetry_hbond_refined 0.131 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 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 8073 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 99
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing