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Crystal structure of catalytic domain of the proto-oncogene tyrosine-protein kinase MER in complex with ADP
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 VAPOR DIFFUSION, HANGING DROP 8.5 290 MER protein (38 mg/mL) was pre-incubated with 2.5 mM ATP and 10 mM MgCl2 for 3 hours at room temperature. Crystals were obtained at 290K against 29% PEG 400, 0.2M MgCl2, and 0.1 M Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.26 45.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.385 α = 90 b = 89.88 β = 103.09 c = 69.537 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 270 Rh coated Si mirrors 2007-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.91790 CHESS F1
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 1.9 25.05 98.3 0.09 24.1 7.2 49802 49802 -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) 1 1.9 1.97 88.7 0.659 2.3929 5.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2P0C 1.9 25.05 49525 47038 2487 98.32 0.19469 0.19221 0.24 0.2558 RANDOM 33.967
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] 6.06 0.38 -2.51 -3.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.761 r_dihedral_angle_4_deg 20.243 r_dihedral_angle_3_deg 15.047 r_dihedral_angle_1_deg 5.58 r_scangle_it 4.712 r_scbond_it 3.602 r_mcangle_it 2.686 r_mcbond_it 1.904 r_angle_refined_deg 1.511 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.761 r_dihedral_angle_4_deg 20.243 r_dihedral_angle_3_deg 15.047 r_dihedral_angle_1_deg 5.58 r_scangle_it 4.712 r_scbond_it 3.602 r_mcangle_it 2.686 r_mcbond_it 1.904 r_angle_refined_deg 1.511 r_nbtor_refined 0.306 r_nbd_refined 0.202 r_symmetry_vdw_refined 0.173 r_xyhbond_nbd_refined 0.137 r_symmetry_hbond_refined 0.121 r_chiral_restr 0.103 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4126 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 67
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling