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Human EphA3 kinase and juxtamembrane region, base, AMP-PNP bound structure
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 33.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.043 α = 90 b = 38.324 β = 102.33 c = 76.514 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 2006-03-23 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 1.6 40 91.7 0.052 30.8 6.6 37433
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) 1.6 1.66 48.7 0.175 4.5 1979
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 1.6 27.83 37417 1882 91.66 0.19 0.189 0.2 0.219 0.2243 RANDOM 17.074
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 34.184 r_dihedral_angle_4_deg 13.693 r_dihedral_angle_3_deg 11.428 r_dihedral_angle_1_deg 5.332 r_scangle_it 2.273 r_scbond_it 1.704 r_angle_refined_deg 1.192 r_mcangle_it 1.064 r_mcbond_it 0.925 r_angle_other_deg 0.812
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.184 r_dihedral_angle_4_deg 13.693 r_dihedral_angle_3_deg 11.428 r_dihedral_angle_1_deg 5.332 r_scangle_it 2.273 r_scbond_it 1.704 r_angle_refined_deg 1.192 r_mcangle_it 1.064 r_mcbond_it 0.925 r_angle_other_deg 0.812 r_symmetry_vdw_refined 0.217 r_nbd_refined 0.206 r_symmetry_vdw_other 0.203 r_nbd_other 0.181 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.148 r_mcbond_other 0.141 r_symmetry_hbond_refined 0.108 r_metal_ion_refined 0.086 r_nbtor_other 0.08 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2303 Nucleic Acid Atoms Solvent Atoms 251 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