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Human EphA3 Kinase and Juxtamembrane Region Bound to Substrate KQWDNYE[pTyr]IW
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, 0.04M Ammonium sulfate, 0.1M Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.77 30.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.463 α = 90 b = 38.201 β = 102.15 c = 76.649 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 2007-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54178
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 1.7 30 98.3 0.044 28.359 3.4 33335
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 1.7 1.76 84.1 0.312 2.4 2839
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 1.7 26.47 33313 1669 98.21 0.168 0.166 0.1773 0.194 0.1741 RANDOM 26.127
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.382 r_dihedral_angle_4_deg 17.281 r_dihedral_angle_3_deg 11.835 r_dihedral_angle_1_deg 5.296 r_scangle_it 2.48 r_scbond_it 1.769 r_angle_refined_deg 1.279 r_mcangle_it 1.098 r_mcbond_it 0.99 r_angle_other_deg 0.862
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.382 r_dihedral_angle_4_deg 17.281 r_dihedral_angle_3_deg 11.835 r_dihedral_angle_1_deg 5.296 r_scangle_it 2.48 r_scbond_it 1.769 r_angle_refined_deg 1.279 r_mcangle_it 1.098 r_mcbond_it 0.99 r_angle_other_deg 0.862 r_symmetry_vdw_other 0.252 r_symmetry_vdw_refined 0.243 r_nbd_refined 0.21 r_nbd_other 0.186 r_nbtor_refined 0.176 r_mcbond_other 0.161 r_xyhbond_nbd_refined 0.131 r_symmetry_hbond_refined 0.108 r_nbtor_other 0.081 r_metal_ion_refined 0.079 r_chiral_restr 0.074 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2379 Nucleic Acid Atoms Solvent Atoms 301 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