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Crystal Structure of Ephrin A2 (ephA2) Receptor Protein Kinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JPA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 Ethylene Glycol, PEG 10K, HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.4 48.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.127 α = 90 b = 72.127 β = 90 c = 241.623 γ = 120
Symmetry Space Group P 32 2 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 4 synchrotron 2001-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 1.0 ALS 5.0.3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.3 40 98 0.057 0.057 11.5 4.1 36207 35483 2 2 44.66
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.36 0.78 0.485 0.485 2 3.8 1662
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1JPA 2.3 40 35483 30548 848 93.7 0.237 0.23619 0.23556 0.28833 RANDOM 44.668
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] 0.89 0.44 0.89 -1.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.46 r_scangle_it 3.579 r_scbond_it 2.079 r_angle_refined_deg 1.695 r_mcangle_it 1.523 r_angle_other_deg 0.895 r_mcbond_it 0.831 r_symmetry_vdw_other 0.245 r_nbd_other 0.234 r_nbd_refined 0.221
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.46 r_scangle_it 3.579 r_scbond_it 2.079 r_angle_refined_deg 1.695 r_mcangle_it 1.523 r_angle_other_deg 0.895 r_mcbond_it 0.831 r_symmetry_vdw_other 0.245 r_nbd_other 0.234 r_nbd_refined 0.221 r_symmetry_hbond_refined 0.184 r_symmetry_vdw_refined 0.173 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.098 r_nbtor_other 0.091 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4221 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 62
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling AMoRE phasing REFMAC refinement CCP4 data scaling