☰ Navigation Tabs
Catalytic Domain of the Proto-oncogene Tyrosine-protein Kinase MER
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2G15 PDB entry 2G15
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 The protein in 20mM Tris-HCl pH 8.0, 0.5M NaCl, 5% glycerol, 2mM BME, 2.5 mM AMP-PNP, 10 mM MgCl2, 5mM peptide (ADEPNYETWG) was mixed with crystallization buffer (15% PEG 8000, 0.2M ammonium sulfate, and 0.1 M Sodium cacodylate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.23 44.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.47 α = 90 b = 90.057 β = 102.44 c = 69.253 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 IMAGE PLATE RIGAKU RAXIS IV++ 2007-01-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54178
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 2.4 25 99.8 0.067 21.6 3.5 24544 24544 -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) 2.4 2.49 99.7 0.293 5.2 3.4 2456
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2G15 2.4 24.79 23326 1232 99.54 0.20761 0.20414 0.204 0.27392 0.2701 RANDOM 39.11
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] 5.72 -0.91 -3.14 -2.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.742 r_dihedral_angle_4_deg 16.83 r_dihedral_angle_3_deg 15.862 r_dihedral_angle_1_deg 5.194 r_scangle_it 2.174 r_scbond_it 1.618 r_mcangle_it 1.316 r_angle_refined_deg 1.201 r_mcbond_it 0.766 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.742 r_dihedral_angle_4_deg 16.83 r_dihedral_angle_3_deg 15.862 r_dihedral_angle_1_deg 5.194 r_scangle_it 2.174 r_scbond_it 1.618 r_mcangle_it 1.316 r_angle_refined_deg 1.201 r_mcbond_it 0.766 r_nbtor_refined 0.299 r_nbd_refined 0.195 r_symmetry_vdw_refined 0.181 r_symmetry_hbond_refined 0.168 r_metal_ion_refined 0.16 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3934 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing