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Mix-and-diffuse serial synchrotron crystallography: structure of N,N',N''-Triacetylchitotriose bound to Lysozyme with 50s time-delay, phased with 4ET8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ET8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 3.5 274 Crystals with sizes between 6 and 8 um in diameter were obtained by adding three parts of precipitant (1M NaCl, 40% ethylene glycol (v/v), 15% PEG4000 (w/v), 50 mM acetate buffer at pH 3.5, filtered through 450 nm filter) to one part of lysozyme (Sigma-Aldrich, 126 mg/ml dissolved in50 mM acetate buffer, pH 3.5, filtered through 100 nm filter) at 274K (ThermoStat C, Eppendorf, Germany). The resulting mixture was immediately subjected to rapid mixing and incubated for 30 minutes at 274K.
Crystal Properties Matthews coefficient Solvent content 2.12 41.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.61 α = 90 b = 79.61 β = 90 c = 38.3 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 295 PIXEL DECTRIS PILATUS3 6M 2016-06-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 0.918 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) R Split (All) 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 1.7 22.681 100 0.99 0.0349 16.65 4932 14040 25.77
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.761 100 0.39 1.1245 1.06 267
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4ET8 1.7 22.681 1.33 14016 1403 99.83 0.1692 0.1661 0.1666 0.1975 0.1964 Same as for 5NJQ
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 9.994 f_angle_d 0.669 f_chiral_restr 0.041 f_bond_d 0.004 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 47
Software Software Software Name Purpose PHENIX refinement CrystFEL data reduction CrystFEL data scaling PHENIX phasing