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Joint neutron and x-ray structure of alginate lyase PsAlg7C soaked with pentamannuronic acid
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8C3X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 30% PEG3350,0.1M Bis-Tris pH 5.5, 0.3M NaCl
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.089 α = 90 b = 61.451 β = 90 c = 91.882 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 neutron 293 SCINTILLATION ORNL ANGER CAMERA 2022-07-12 L LAUE 2 2 x-ray 293 PIXEL DECTRIS EIGER R 4M 2022-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SPALLATION SOURCE ORNL Spallation Neutron Source BEAMLINE MANDI 2-4 ORNL Spallation Neutron Source MANDI 2 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.15 14.57 94.61 0.22 0.1 0.94 8.2 4.7 12772 2 2.1 27.42 100 0.12 0.05 0.99 12.4 6.3 14513
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.22 0.27 0.14 0.27 3.3 2 2.1 2.16 0.66 0.29 0.8 4
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 2.15 14.57 12760 632 94.76 0.2371 0.2349 0.2767 19.74 X-RAY DIFFRACTION MOLECULAR REPLACEMENT 2.1 27.41 14460 726 99.93 0.1303 0.1279 0.3531 0.1745 0.3576
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_bond_d 0.0129
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1768 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 61