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Human EphA3 kinase and juxtamembrane region, dephosphorylated, 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 1.82 32.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.736 α = 90 b = 38.225 β = 102.04 c = 76.029 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 1.6 25 92.5 0.045 12.2 2.6 37319
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 1.6 1.66 49.2 0.464 1.6 1967
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 1.605 22.46 37308 1895 93.68 0.186 0.184 0.1908 0.224 0.2264 RANDOM 18.383
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 33.949 r_dihedral_angle_4_deg 12.989 r_dihedral_angle_3_deg 11.908 r_dihedral_angle_1_deg 5.193 r_scangle_it 2.362 r_scbond_it 1.725 r_angle_refined_deg 1.287 r_mcangle_it 1.037 r_angle_other_deg 1.025 r_mcbond_it 0.922
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.949 r_dihedral_angle_4_deg 12.989 r_dihedral_angle_3_deg 11.908 r_dihedral_angle_1_deg 5.193 r_scangle_it 2.362 r_scbond_it 1.725 r_angle_refined_deg 1.287 r_mcangle_it 1.037 r_angle_other_deg 1.025 r_mcbond_it 0.922 r_nbd_refined 0.211 r_nbd_other 0.184 r_nbtor_refined 0.177 r_symmetry_vdw_other 0.174 r_symmetry_vdw_refined 0.17 r_mcbond_other 0.167 r_xyhbond_nbd_refined 0.157 r_chiral_restr 0.132 r_symmetry_hbond_refined 0.117 r_nbtor_other 0.081 r_metal_ion_refined 0.045 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2219 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 48
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