☰ Navigation Tabs
Crystal Structure of the EphA4-ephrinA2 complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KGY PDB ENTRY 1KGY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 20% PEG 3350, 200 MM KNO3, pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.9 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.412 α = 90 b = 115.412 β = 90 c = 59.354 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 CCD MIRRORS 2007-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 2.35 50 99.9 0.09 30 16 18961 -3 58.9
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 2.35 2.41 99.4 0.75 1.8 8.1
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 1KGY 2.35 49.97 17987 954 99.9 0.20012 0.19779 0.2089 0.24554 0.2605 RANDOM 42.79
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] 1.19 0.59 1.19 -1.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.513 r_dihedral_angle_3_deg 15.017 r_dihedral_angle_4_deg 13.384 r_dihedral_angle_1_deg 6.389 r_scangle_it 2.644 r_scbond_it 1.56 r_mcangle_it 1.409 r_angle_refined_deg 1.287 r_angle_other_deg 0.807 r_mcbond_it 0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.513 r_dihedral_angle_3_deg 15.017 r_dihedral_angle_4_deg 13.384 r_dihedral_angle_1_deg 6.389 r_scangle_it 2.644 r_scbond_it 1.56 r_mcangle_it 1.409 r_angle_refined_deg 1.287 r_angle_other_deg 0.807 r_mcbond_it 0.75 r_mcbond_other 0.099 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2576 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing