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Human EphA3 kinase and juxtamembrane region, Y602F 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 33.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.215 α = 90 b = 38.289 β = 102.43 c = 76.004 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 1.15 40 99.5 0.036 13.2 3.9 107783
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) 1.15 1.19 99.7 0.625 3.6 10706
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 1.15 23.4 107702 5412 99.4 0.193 0.192 0.1997 0.206 0.1991 RANDOM 13.523
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 32.701 r_dihedral_angle_4_deg 13.927 r_dihedral_angle_3_deg 11.14 r_dihedral_angle_1_deg 4.958 r_scangle_it 1.947 r_scbond_it 1.53 r_angle_refined_deg 1.139 r_mcangle_it 1.039 r_mcbond_it 0.864 r_angle_other_deg 0.819
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.701 r_dihedral_angle_4_deg 13.927 r_dihedral_angle_3_deg 11.14 r_dihedral_angle_1_deg 4.958 r_scangle_it 1.947 r_scbond_it 1.53 r_angle_refined_deg 1.139 r_mcangle_it 1.039 r_mcbond_it 0.864 r_angle_other_deg 0.819 r_symmetry_vdw_refined 0.212 r_nbd_refined 0.207 r_nbd_other 0.179 r_nbtor_refined 0.176 r_symmetry_vdw_other 0.174 r_mcbond_other 0.138 r_symmetry_hbond_refined 0.134 r_xyhbond_nbd_refined 0.126 r_nbtor_other 0.083 r_chiral_restr 0.068 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 2305 Nucleic Acid Atoms Solvent Atoms 370 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