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Human EphA3 Kinase and Juxtamembrane Region Bound to Substrate KQWDNYEFIW
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FXX PDB ENTRY 3FXX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 20 mg/mL Protein, 25% PEG 3350, 0.04M Ammonium sulfate, 0.1M Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.8 30.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.824 α = 90 b = 38.261 β = 102.05 c = 76.365 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 2008-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.78 34.04 100 0.049 0.049 7.855 3.6 29459 29456 21.842
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.78 1.88 100 0.224 0.224 3.3 3.5 4266
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 3FXX 1.8 26.73 28393 1430 99.37 0.181 0.179 0.1873 0.212 0.2129 RANDOM 29.522
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.494 r_dihedral_angle_4_deg 19.878 r_dihedral_angle_3_deg 12.808 r_dihedral_angle_1_deg 5.41 r_scangle_it 2.723 r_scbond_it 2.002 r_mcangle_it 1.271 r_angle_refined_deg 1.259 r_mcbond_it 1.117 r_angle_other_deg 0.871
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.494 r_dihedral_angle_4_deg 19.878 r_dihedral_angle_3_deg 12.808 r_dihedral_angle_1_deg 5.41 r_scangle_it 2.723 r_scbond_it 2.002 r_mcangle_it 1.271 r_angle_refined_deg 1.259 r_mcbond_it 1.117 r_angle_other_deg 0.871 r_nbd_refined 0.209 r_symmetry_vdw_other 0.189 r_nbd_other 0.186 r_mcbond_other 0.179 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.13 r_symmetry_hbond_refined 0.122 r_symmetry_vdw_refined 0.12 r_nbtor_other 0.082 r_chiral_restr 0.075 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2345 Nucleic Acid Atoms Solvent Atoms 233 Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection