☰ Navigation Tabs
Human EphA3 kinase domain, phosphorylated, AMP-PNP bound structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QOB PDB entry 2QOB
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 2 38.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.79 α = 90 b = 38.337 β = 102.07 c = 76.439 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 2006-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.97900 CHESS A1
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 1.25 50 99.6 0.05 13.6 3.6 84007
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) 1.25 1.29 98.6 0.25 3.3 8276
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 2QOB 1.25 27.45 82459 4110 97.42 0.17 0.169 0.1768 0.186 0.1953 RANDOM 10.324
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 29.923 r_dihedral_angle_4_deg 15.181 r_dihedral_angle_3_deg 10.641 r_dihedral_angle_1_deg 5.17 r_scangle_it 1.9 r_angle_refined_deg 1.673 r_scbond_it 1.466 r_mcangle_it 0.902 r_angle_other_deg 0.86 r_mcbond_it 0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.923 r_dihedral_angle_4_deg 15.181 r_dihedral_angle_3_deg 10.641 r_dihedral_angle_1_deg 5.17 r_scangle_it 1.9 r_angle_refined_deg 1.673 r_scbond_it 1.466 r_mcangle_it 0.902 r_angle_other_deg 0.86 r_mcbond_it 0.76 r_metal_ion_refined 0.294 r_nbd_refined 0.233 r_symmetry_vdw_other 0.219 r_nbd_other 0.182 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.168 r_symmetry_hbond_refined 0.143 r_symmetry_vdw_refined 0.126 r_mcbond_other 0.121 r_nbtor_other 0.082 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2483 Nucleic Acid Atoms Solvent Atoms 427 Heterogen Atoms 42
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