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Crystal structure of the catalytic domain of the proto-oncogene tyrosine-protein kinase MER in complex with inhibitor UNC569
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BRB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 288 Protein: 32.5 mg/mL in 20 mM Tris pH 8.0, 500mM sodium chloride, 2mM beta-mercaptoethanol; incubated with inhibitor (2.5 mM final concentration) overnight; Mixed 1:1 with crystallization solution (27-33% (v/v) Peg400, 200 mM magnesium chloride, 100 mM Tris pH 8.5), VAPOR DIFFUSION, SITTING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.18 43.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.158 α = 90 b = 91.142 β = 100.35 c = 68.356 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 MARMOSAIC 300 mm CCD 2010-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID APS 22-ID
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 2.69 29.02 96.3 0.098 14.7 3.6 16603 -3 62.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.69 2.72 59.3 0.522 1.5 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 3BRB 2.69 29.02 -3 16603 15728 840 95.9 0.228 0.225 0.2228 0.298 0.2886 RANDOM 57.62
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] 7.16 -0.95 -4.01 -3.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.371 r_dihedral_angle_3_deg 15.685 r_dihedral_angle_4_deg 13.496 r_dihedral_angle_1_deg 4.983 r_scangle_it 1.156 r_angle_refined_deg 1.147 r_scbond_it 0.708 r_mcangle_it 0.449 r_mcbond_it 0.235 r_chiral_restr 0.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.371 r_dihedral_angle_3_deg 15.685 r_dihedral_angle_4_deg 13.496 r_dihedral_angle_1_deg 4.983 r_scangle_it 1.156 r_angle_refined_deg 1.147 r_scbond_it 0.708 r_mcangle_it 0.449 r_mcbond_it 0.235 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 4059 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms 64
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling