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Crystal Structure of the EphA4 Ligand Binding Domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NUK PDB ENTRY 1NUK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 30% PEG 4000, 8% PROPAN-1-OL, AND 100 MM TRIS PH 8.5
Crystal Properties Matthews coefficient Solvent content 2.2 45.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.736 α = 90 b = 73.228 β = 98.35 c = 54.42 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 IMAGE PLATE MAR scanner 345 mm plate MIRRORS 2005-12-04 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 1.85 25 98.2 0.07 19.5 3.7 31875 -3 26.2
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 1.85 1.9 97.4 0.34 4 3.7
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 1NUK 1.85 23.75 30277 1595 98.2 0.18921 0.18682 0.2139 0.23379 0.2488 RANDOM 31.744
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] 1.34 0.3 -1.17 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.897 r_dihedral_angle_4_deg 15.184 r_dihedral_angle_3_deg 15.03 r_dihedral_angle_1_deg 6.659 r_scangle_it 2.923 r_scbond_it 1.776 r_mcangle_it 1.424 r_angle_refined_deg 1.246 r_mcbond_it 0.786 r_angle_other_deg 0.771
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.897 r_dihedral_angle_4_deg 15.184 r_dihedral_angle_3_deg 15.03 r_dihedral_angle_1_deg 6.659 r_scangle_it 2.923 r_scbond_it 1.776 r_mcangle_it 1.424 r_angle_refined_deg 1.246 r_mcbond_it 0.786 r_angle_other_deg 0.771 r_mcbond_other 0.177 r_chiral_restr 0.074 r_bond_refined_d 0.01 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 2890 Nucleic Acid Atoms Solvent Atoms 297 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing