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Crystal Structure of the EphA4-ephrinB2 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 6 30% PEG 6000, 1 M LITHIUM CHLORIDE, AND 100 MM MES PH 6.0
Crystal Properties Matthews coefficient Solvent content 2 39.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.371 α = 90 b = 107.371 β = 90 c = 47.619 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 IMAGE PLATE MAR scanner 345 mm plate MIRRORS 2006-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 2.45 30 99.3 0.05 43.2 11.7 11645 -3 60.9
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 2.45 2.54 94.2 0.53 2.6 6.6
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 2.45 28 11062 564 99.37 0.21784 0.21565 0.2302 0.26021 0.2694 RANDOM 49.394
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] -0.9 -0.45 -0.9 1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.651 r_dihedral_angle_3_deg 13.628 r_dihedral_angle_4_deg 13.187 r_dihedral_angle_1_deg 6.207 r_scangle_it 1.235 r_angle_refined_deg 1.064 r_angle_other_deg 0.727 r_scbond_it 0.704 r_mcangle_it 0.561 r_mcbond_it 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.651 r_dihedral_angle_3_deg 13.628 r_dihedral_angle_4_deg 13.187 r_dihedral_angle_1_deg 6.207 r_scangle_it 1.235 r_angle_refined_deg 1.064 r_angle_other_deg 0.727 r_scbond_it 0.704 r_mcangle_it 0.561 r_mcbond_it 0.295 r_chiral_restr 0.065 r_mcbond_other 0.036 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 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 2533 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing