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LASV cap-snatching endonuclease in complex with BXA - serial synchrotron crystallography
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MIW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 293 After limited proteolysis with subtilisin A, 7.5 mg/ml target protein were mixed with an equal volume of crystallization solution (10% w/v PEG 10000, 250 mM MgSO4 and 100 mM Tris/HCl pH 9.0)
Crystal Properties Matthews coefficient Solvent content 2.54 51.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.63 α = 90 b = 58.63 β = 90 c = 135.57 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 PIXEL DECTRIS PILATUS 6M 2024-12-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P09 HiPhaX 0.7749 PETRA III, DESY P09 HiPhaX
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 1.82 45.19 100 0.978 6.4 94.4 22818 24.69
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 1.82 1.85 0.709
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 1.82 44.34 1.33 22003 1999 99.91 0.2008 0.1973 0.198 0.2359 0.2366 33
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 14.7058 f_angle_d 1.2075 f_chiral_restr 0.0681 f_plane_restr 0.014 f_bond_d 0.0123
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1373 Nucleic Acid Atoms Solvent Atoms 70 Heterogen Atoms 44
Software Software Software Name Purpose PHENIX refinement CrystFEL data reduction CrystFEL data scaling PHENIX phasing