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X-ray Crystal structure of glycoside hydrolase family 18 chitinase from Serratia marcescens hexahistigine-tagged SmChiB with triacetyl chitotriose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WD3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 293 di-ammonium phosphate, sodium acetate
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.38 α = 90 b = 97.38 β = 90 c = 197.347 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 95 PIXEL DECTRIS PILATUS3 S 6M 2022-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 1.43 48.69 99.93 0.06641 0.06903 0.01872 1 19.72 13.4 344210 19.39
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 1.43 1.481 99.93 1.723 1.791 0.4864 0.757 1.61 13.4
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 1.43 48.69 1.33 343985 2008 99.93 0.1239 0.1238 0.1249 0.1382 0.1384 28.95
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 9.4897 f_angle_d 0.837 f_chiral_restr 0.0802 f_plane_restr 0.0073 f_bond_d 0.0061
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7831 Nucleic Acid Atoms Solvent Atoms 1581 Heterogen Atoms 590
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction XDS data scaling PHASER phasing