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Human EphA3 kinase and juxtamembrane region, phosphorylated, AMP-PNP bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GSF PDB entry 2GSF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 20 mg/mL Protein, 25% PEG 3350, 0.2M Ammonium sulfate, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.83 32.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.839 α = 90 b = 38.205 β = 102.16 c = 76.474 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 200 IMAGE PLATE RIGAKU RAXIS IV++ 2006-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT
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 1.55 20 98.4 0.038 36.4 5.9 42955
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) 1.55 1.63 92.2 0.134 4.4 1837
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 2GSF 1.55 18.51 42955 2150 100 0.183 0.182 0.1892 0.211 0.2143 RANDOM 14.846
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 29.233 r_dihedral_angle_4_deg 17.801 r_dihedral_angle_3_deg 12.432 r_dihedral_angle_1_deg 5.089 r_scangle_it 2.766 r_scbond_it 2.104 r_angle_refined_deg 1.375 r_mcangle_it 1.326 r_mcbond_it 1.13 r_angle_other_deg 0.872
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.233 r_dihedral_angle_4_deg 17.801 r_dihedral_angle_3_deg 12.432 r_dihedral_angle_1_deg 5.089 r_scangle_it 2.766 r_scbond_it 2.104 r_angle_refined_deg 1.375 r_mcangle_it 1.326 r_mcbond_it 1.13 r_angle_other_deg 0.872 r_symmetry_vdw_other 0.254 r_mcbond_other 0.231 r_nbd_refined 0.216 r_nbd_other 0.192 r_nbtor_refined 0.18 r_symmetry_vdw_refined 0.168 r_xyhbond_nbd_refined 0.154 r_symmetry_hbond_refined 0.149 r_chiral_restr 0.081 r_nbtor_other 0.081 r_metal_ion_refined 0.037 r_bond_refined_d 0.012 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 2291 Nucleic Acid Atoms Solvent Atoms 418 Heterogen Atoms 32
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-2000 data reduction HKL-2000 data scaling