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Human EphA3 kinase and juxtamembrane region, dephosphorylated, apo 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 1.85 33.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.449 α = 90 b = 38.359 β = 102.63 c = 76.226 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 2006-11-04 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 20 45.1 0.032 22.3 1.2 38458
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 19 0.092 1.1 769
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 19.18 37087 1881 90.73 0.177 0.176 0.1844 0.203 0.2038 RANDOM 13.738
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 32.582 r_dihedral_angle_4_deg 13.768 r_dihedral_angle_3_deg 11.462 r_dihedral_angle_1_deg 5.759 r_scangle_it 2.092 r_scbond_it 1.508 r_angle_refined_deg 1.182 r_mcangle_it 0.937 r_angle_other_deg 0.834 r_mcbond_it 0.802
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.582 r_dihedral_angle_4_deg 13.768 r_dihedral_angle_3_deg 11.462 r_dihedral_angle_1_deg 5.759 r_scangle_it 2.092 r_scbond_it 1.508 r_angle_refined_deg 1.182 r_mcangle_it 0.937 r_angle_other_deg 0.834 r_mcbond_it 0.802 r_nbd_refined 0.215 r_symmetry_vdw_refined 0.209 r_nbd_other 0.178 r_nbtor_refined 0.175 r_symmetry_vdw_other 0.172 r_xyhbond_nbd_refined 0.156 r_mcbond_other 0.13 r_symmetry_hbond_refined 0.127 r_xyhbond_nbd_other 0.092 r_nbtor_other 0.082 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2349 Nucleic Acid Atoms Solvent Atoms 335 Heterogen Atoms 4
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