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Kinase domain of human ephrin type-A receptor 7 (Epha7)
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 7 298 Well solution: 20% PEG 3350, 0.2 M NH4 formate, 0.1 M HEPES pH 7.0. Protein solution: 12 mg/mL. Drops: 1:1 ratio of well:protein solution. Crystals cryoprotected by transfer to drop containing mother liquor to which MPD was added to 25%, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.31 46.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.88 α = 90 b = 51.88 β = 90 c = 215.5 γ = 120
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 315 MIRRORS 2007-08-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 45 100 0.065 41.8 10.7 43283 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.6 1.66 100 0.52 3.8 6.9
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 44.95 40895 2171 99.97 0.1637 0.16255 0.1628 0.18678 0.1875 RANDOM 30.703
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] 0.52 0.26 0.52 -0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.121 r_dihedral_angle_4_deg 20.203 r_dihedral_angle_3_deg 12.462 r_dihedral_angle_1_deg 5.247 r_scangle_it 3.049 r_scbond_it 1.944 r_angle_refined_deg 1.208 r_mcangle_it 1.047 r_mcbond_it 0.674 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.121 r_dihedral_angle_4_deg 20.203 r_dihedral_angle_3_deg 12.462 r_dihedral_angle_1_deg 5.247 r_scangle_it 3.049 r_scbond_it 1.944 r_angle_refined_deg 1.208 r_mcangle_it 1.047 r_mcbond_it 0.674 r_nbtor_refined 0.308 r_symmetry_hbond_refined 0.216 r_nbd_refined 0.205 r_symmetry_vdw_refined 0.185 r_xyhbond_nbd_refined 0.115 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2249 Nucleic Acid Atoms Solvent Atoms 300 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing