☰ Navigation Tabs
Crystal structure of the human ephrin A2- ephrin A1 complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C8X PDB ENTRIES 3C8X, 1SHW experimental model PDB 1SHW PDB ENTRIES 3C8X, 1SHW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 290.9 14.9% PEG 4000, 0.1M Sodium citrate pH 5.6, 20% Isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 290.9K, pH 5.60
Crystal Properties Matthews coefficient Solvent content 3.24 62.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.431 α = 90 b = 99.431 β = 90 c = 204.879 γ = 120
Symmetry Space Group P 65 2 2
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 2008-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT
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 2.65 25 100 0.109 35.74 20.8 18122 -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 2.65 2.74 100 0.714 5.509 21.2
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 ENTRIES 3C8X, 1SHW 2.65 24.86 17120 938 99.94 0.19507 0.19343 0.1941 0.22533 0.2301 RANDOM 42.445
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] 0.19 0.09 0.19 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.89 r_dihedral_angle_3_deg 16.557 r_dihedral_angle_4_deg 15.66 r_dihedral_angle_1_deg 6.59 r_scangle_it 3.59 r_scbond_it 2.206 r_mcangle_it 1.703 r_angle_refined_deg 1.225 r_mcbond_it 1.006 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.89 r_dihedral_angle_3_deg 16.557 r_dihedral_angle_4_deg 15.66 r_dihedral_angle_1_deg 6.59 r_scangle_it 3.59 r_scbond_it 2.206 r_mcangle_it 1.703 r_angle_refined_deg 1.225 r_mcbond_it 1.006 r_nbtor_refined 0.313 r_symmetry_hbond_refined 0.219 r_nbd_refined 0.191 r_symmetry_vdw_refined 0.154 r_xyhbond_nbd_refined 0.102 r_chiral_restr 0.087 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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 2473 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms 39
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling