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Crystal structure of human Schlafen 5 N'-terminal domain (SLFN5-N) involved in ssRNA cleaving and DNA binding
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5YD0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277.15 100 mM Tris, pH 7.5, 80 mM magnesium chloride, 1.6 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 4.55 72.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 211.86 α = 90 b = 156.442 β = 110.382 c = 131.459 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 87.15 PIXEL DECTRIS PILATUS3 6M 2019-06-27 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9785 SSRF BL19U1
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 fixed target
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3.294 50 90.2 1 13.5 6.8 43847 80
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.3 3.61 0.731
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 5YD0 3.29477066393 41.0761808916 1.34999900373 43638 2162 71.9161489148 0.203555713424 0.201355733206 0.2061 0.247153773675 0.2504 70
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 3.23155903385 f_angle_d 0.758545511386 f_chiral_restr 0.0462753104805 f_plane_restr 0.00398805901482 f_bond_d 0.0028929713363
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14069 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 6
Software Software Software Name Purpose PHENIX refinement REFMAC refinement XDS data reduction STARANISO data scaling PHASER phasing