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Crystal structure of kinase domain of protein tyrosine kinase 2 beta (PTK2B)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ETM PDB entry 2ETM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277 0.05M Magnesium chloride, 0.1M Bis-tris, 17.5% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.39 48.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.45 α = 90 b = 96.14 β = 93.66 c = 43.2 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 315 2007-09-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9753 ESRF ID29
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 1.6 18.84 99.9 0.081 16.22 7.4 49357 40123 -3 22.575
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 1.6 1.7 100 0.441 4.6
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 (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 PDB entry 2ETM 1.6 18.84 40120 40120 3209 100 0.187 0.187 0.184 0.1823 0.219 0.2173 RANDOM 20.195
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] -0.01 0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.943 r_dihedral_angle_4_deg 18.001 r_dihedral_angle_3_deg 14.472 r_dihedral_angle_1_deg 5.086 r_scangle_it 1.995 r_mcangle_it 1.984 r_scbond_it 1.305 r_angle_refined_deg 1.279 r_mcbond_it 1.233 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.943 r_dihedral_angle_4_deg 18.001 r_dihedral_angle_3_deg 14.472 r_dihedral_angle_1_deg 5.086 r_scangle_it 1.995 r_mcangle_it 1.984 r_scbond_it 1.305 r_angle_refined_deg 1.279 r_mcbond_it 1.233 r_nbtor_refined 0.307 r_symmetry_hbond_refined 0.233 r_nbd_refined 0.211 r_symmetry_vdw_refined 0.151 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.086 r_metal_ion_refined 0.041 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2183 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 7
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MxCuBE data collection XDS data reduction