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Semaphorin-5A TSR 3-4 domains in complex with sulfate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 30% PEG 4000, 0.2 M lithium sulfate, 0.1 M Tris 2 VAPOR DIFFUSION, SITTING DROP 8.5 293 30% PEG 4000, 0.2 M lithium sulfate, 0.1 M Tris
Crystal Properties Matthews coefficient Solvent content 2.43 49.5 2.43 49.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.081 α = 90 b = 29.286 β = 100.46 c = 90.429 γ = 90
Symmetry Space Group C 1 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 PIXEL DECTRIS PILATUS3 6M 2020-01-26 M SINGLE WAVELENGTH 2 2 x-ray 50 PIXEL DECTRIS PILATUS 12M 2020-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24 2 SYNCHROTRON DIAMOND BEAMLINE I23 2.7552 Diamond I23
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 1.714 88.925 70.7 0.096 0.041 0.995 9.3 6.2 20985 29.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.714 1.855 16.9 1.2 0.7 0.338 1 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION SAD FREE R-VALUE 1.714 51.67 1.35 20984 1000 70.62 0.2072 0.206 0.2056 0.2312 0.2307
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.701 f_angle_d 0.872 f_chiral_restr 0.05 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1645 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 54
Software Software Software Name Purpose autoPROC data processing CRANK2 phasing PHENIX refinement Coot model building XDS data reduction Aimless data scaling