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Human EphA3 kinase and juxtamembrane region, Y596:Y602:S768G triple mutant
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 1.84 33.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.303 α = 90 b = 38.292 β = 102.15 c = 75.877 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 210 2006-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.00000 APS 17-ID
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 1.07 40 92.6 0.038 18.9 3.8 124762
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) 1.07 1.09 57.4 0.47 2.3
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 1.07 26.55 124693 6252 100 0.19623 0.19544 0.2027 0.21135 0.2195 RANDOM 11.7
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 31.103 r_dihedral_angle_4_deg 13.207 r_dihedral_angle_3_deg 11.228 r_dihedral_angle_1_deg 4.669 r_scangle_it 1.619 r_scbond_it 1.275 r_angle_refined_deg 1.141 r_angle_other_deg 0.92 r_mcangle_it 0.908 r_mcbond_it 0.763
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.103 r_dihedral_angle_4_deg 13.207 r_dihedral_angle_3_deg 11.228 r_dihedral_angle_1_deg 4.669 r_scangle_it 1.619 r_scbond_it 1.275 r_angle_refined_deg 1.141 r_angle_other_deg 0.92 r_mcangle_it 0.908 r_mcbond_it 0.763 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.188 r_symmetry_vdw_other 0.183 r_nbd_other 0.175 r_nbtor_refined 0.175 r_chiral_restr 0.167 r_xyhbond_nbd_refined 0.121 r_mcbond_other 0.117 r_symmetry_hbond_refined 0.104 r_nbtor_other 0.082 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2375 Nucleic Acid Atoms Solvent Atoms 422 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction HKL-2000 data scaling