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Crystal form of Netrin-1 mimics nanotubes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7LRF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 40% v/v 2-methyl-2,4-pentanediol; 5% w/v polyethylene glycol 8000; 100 mM 2-(N-morpholino)ethanesulfonic acid; pH 6.5
Crystal Properties Matthews coefficient Solvent content 4.53 72.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 189.26 α = 90 b = 189.26 β = 90 c = 45.88 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 RIGAKU RAXIS IV++ Rigaku Osmic Confocal Max-Flux multilayer mirror 2017-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54187
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 3.4 35.77 68.9 0.412 0.435 0.14 0.994 4.9 9.6 9185 83.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.4 4.2 33.53 1.473 1.553 0.488 0.583 1.9 9.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3.4 35.77 9185 743 68.74 0.3 0.2967 0.2904 0.3348 0.3252 Random selection 88.104
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] -4.198 -2.099 -4.198 13.618
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.949 r_dihedral_angle_6_deg 14.042 r_dihedral_angle_1_deg 10.352 r_dihedral_angle_other_1_deg 8.932 r_dihedral_angle_2_deg 7.406 r_lrange_it 2.853 r_lrange_other 2.853 r_angle_refined_deg 1.847 r_scangle_it 1.532 r_scangle_other 1.532
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.949 r_dihedral_angle_6_deg 14.042 r_dihedral_angle_1_deg 10.352 r_dihedral_angle_other_1_deg 8.932 r_dihedral_angle_2_deg 7.406 r_lrange_it 2.853 r_lrange_other 2.853 r_angle_refined_deg 1.847 r_scangle_it 1.532 r_scangle_other 1.532 r_scbond_it 0.864 r_scbond_other 0.864 r_mcangle_it 0.61 r_mcangle_other 0.61 r_angle_other_deg 0.6 r_dihedral_angle_other_3_deg 0.478 r_mcbond_it 0.338 r_mcbond_other 0.338 r_xyhbond_nbd_refined 0.281 r_symmetry_nbd_other 0.195 r_symmetry_xyhbond_nbd_refined 0.182 r_nbd_refined 0.181 r_nbtor_refined 0.174 r_symmetry_xyhbond_nbd_other 0.162 r_nbd_other 0.162 r_symmetry_nbtor_other 0.107 r_symmetry_nbd_refined 0.105 r_chiral_restr 0.057 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3272 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms 225
Software Software Software Name Purpose REFMAC refinement HKL-3000 data collection XDS data reduction XSCALE data scaling PHASER phasing Coot model building