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X-ray Crystal Structure of Mouse Netrin-1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.7 293 0.1 M HEPES, 2.7-2.8 M NaCl, 0.02-0.2 M glycine, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.8 74.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.754 α = 90 b = 69.754 β = 90 c = 334.802 γ = 120
Symmetry Space Group P 32 2 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 CCD RAYONIX MX-300 vertical collimating mirror, toroidal focusing mirror 2011-10-14 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD RAYONIX MX-225 dynamically bendable mirror 2005-10-12 M SIRAS
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 1.25440 CLSI 08B1-1 2 SYNCHROTRON SLS BEAMLINE X06SA 1.25470, 1.25520, 1.24210 SLS X06SA
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 2.5 50 80.9 0.129 8.8 10.5 27279 27279 60.1
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SIRAS THROUGHOUT 2.64 50 24458 1308 89.45 0.233 0.23 0.2371 0.288 0.2378 RANDOM 64.552
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] -0.84 -0.42 -0.84 2.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.259 r_dihedral_angle_3_deg 18.164 r_dihedral_angle_4_deg 15.243 r_dihedral_angle_1_deg 13.261 r_mcangle_it 5.951 r_scbond_it 3.878 r_mcbond_other 3.622 r_mcbond_it 3.621 r_angle_refined_deg 1.806 r_angle_other_deg 0.857
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.259 r_dihedral_angle_3_deg 18.164 r_dihedral_angle_4_deg 15.243 r_dihedral_angle_1_deg 13.261 r_mcangle_it 5.951 r_scbond_it 3.878 r_mcbond_other 3.622 r_mcbond_it 3.621 r_angle_refined_deg 1.806 r_angle_other_deg 0.857 r_chiral_restr 0.086 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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_it 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 3309 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 105
Software Software Software Name Purpose HKL-2000 data collection SHARP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling