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Human EphA3 kinase and juxtamembrane region, Y596F 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 33.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.322 α = 90 b = 38.281 β = 102.37 c = 76.079 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 1.2 50 99.9 0.059 12.5 4 95805
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) 1.2 1.24 100 0.713 3.7 9519
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 1.2 34.06 95380 4782 100 0.182 0.181 0.1891 0.195 0.2046 RANDOM 12.56
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 34.177 r_dihedral_angle_4_deg 13.242 r_dihedral_angle_3_deg 10.404 r_dihedral_angle_1_deg 5.222 r_scangle_it 2.028 r_scbond_it 1.568 r_angle_other_deg 1.225 r_angle_refined_deg 1.209 r_mcangle_it 1.024 r_mcbond_it 0.887
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.177 r_dihedral_angle_4_deg 13.242 r_dihedral_angle_3_deg 10.404 r_dihedral_angle_1_deg 5.222 r_scangle_it 2.028 r_scbond_it 1.568 r_angle_other_deg 1.225 r_angle_refined_deg 1.209 r_mcangle_it 1.024 r_mcbond_it 0.887 r_nbd_refined 0.209 r_symmetry_vdw_other 0.192 r_symmetry_vdw_refined 0.183 r_nbd_other 0.177 r_nbtor_refined 0.175 r_chiral_restr 0.147 r_mcbond_other 0.138 r_xyhbond_nbd_refined 0.127 r_nbtor_other 0.085 r_symmetry_hbond_refined 0.067 r_bond_refined_d 0.007 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 2378 Nucleic Acid Atoms Solvent Atoms 459 Heterogen Atoms 4
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