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Structure of the ternary complex between Netrin-1, Repulsive-Guidance Molecule-B (RGMB) and Neogenin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BQ6 4BQ6, 1X5I, 4PLM experimental model PDB 1X5I 4BQ6, 1X5I, 4PLM experimental model PDB 4PLM 4BQ6, 1X5I, 4PLM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298.15 0.1 M imidazole/MES pH 6.5, 10% (w/v) PEG 8000, 20% (v/v) ethylene glycol, 30 mM sodium nitrate, 30 mM sodium phosphate, 30 mM ammonium sulphate
Crystal Properties Matthews coefficient Solvent content 3.49 64.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.78 α = 90 b = 136.78 β = 90 c = 430.11 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 PIXEL DECTRIS EIGER2 X 16M 2015-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97630 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 3.25 79.62 99.9 0.167 0.046 0.999 16.7 8.1 24856
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.25 3.31 99.6 0.321 1.2
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 4BQ6, 1X5I, 4PLM 3.25 48.96 24847 1275 99.9 0.25 0.249 0.2723 0.263 0.2943 RANDOM 162.9
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] -8.207 -8.207 16.414
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.31 t_omega_torsion 1.69 t_angle_deg 0.97 t_bond_d 0.007 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.31 t_omega_torsion 1.69 t_angle_deg 0.97 t_bond_d 0.007 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6971 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 282
Software Software Software Name Purpose BUSTER refinement PDB_EXTRACT data extraction xia2 data reduction Aimless data scaling PHASER phasing Coot model building