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Semaphorin-5A TSR 3-4 domains in complex with sucrose octasulfate (SOS)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8CKG 8CKG contains the same protein construct, complexed with sulfate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 8 % PEG 8000, 0.1 M sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.41 48.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.106 α = 90 b = 30.77 β = 99.97 c = 84.172 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 2020-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
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 2.56 82.9 55.9 0.143 0.156 0.061 0.994 8.2 6.6 5008 73.54
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 2.561 2.841 10.7 2.67 2.889 1.091 0.098 0.8 6.6
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 MOLECULAR REPLACEMENT FREE R-VALUE 2.56 82.9 1.34 4996 239 55.77 0.2566 0.2554 0.2541 0.285 0.285 82.26
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 11.3601 f_angle_d 0.5615 f_chiral_restr 0.0387 f_plane_restr 0.0047 f_bond_d 0.0018
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1515 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 99
Software Software Software Name Purpose PHENIX refinement autoPROC data processing PHASER phasing Coot model building XDS data reduction Aimless data scaling