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Semaphorin-5A TSR 3-4 domains in complex with nitrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8CKG D_1292128352, same protein complexed with sulfate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.1 M BIS-TRIS propane, 6 M ammonium nitrate
Crystal Properties Matthews coefficient Solvent content 2.7 54.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.894 α = 90 b = 68.347 β = 90 c = 85.502 γ = 90
Symmetry Space Group P 21 21 21
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
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
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 1.557 53.39 55.4 0.123 0.128 0.036 0.996 11.2 12.7 24530 22.67
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 1.557 1.768 8.9 1.564 1.633 0.465 0.624 1.9 12.2
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 1.56 42.75 1.34 24526 1194 55.8 0.1981 0.1966 0.196 0.2292 0.2281 35.52
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 10.2727 f_angle_d 0.6292 f_chiral_restr 0.0412 f_plane_restr 0.0043 f_bond_d 0.0024
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1808 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 112
Software Software Software Name Purpose autoPROC data processing PHENIX refinement Coot model building XDS data reduction Aimless data scaling PHASER phasing