☰ Navigation Tabs
Crystal structure of Aeromonas salmonicida putative carbohydrate binding module and split domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold An AlphaFold3 model was generated locally and used as the search model for molecular replacement. The model was not taken from the AlphaFold Protein Structure Database (no accession code available)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 293 20% w/v PEG 6000, 0.2M Calcium chloride, 5% w/v n-Octyl-B-D-glucoside, 0.1M MES
Crystal Properties Matthews coefficient Solvent content 2.05 40.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.279 α = 90 b = 81.231 β = 99.025 c = 56.133 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2025-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 2.2909
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 2.5 45.791 99.7 0.113 0.129 0.134 0.072 0.993 0.079 13.9 6.2 9640 11.347
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) 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 2.5 2.6 98.3 0.435 0.473 0.521 0.284 0.912 0.285 4.3 6.1
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 2.5 45.79 1.37 9585 491 99.44 0.2248 0.2196 0.2196 0.3156 0.3145 19.8
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 16.4855 f_angle_d 1.0822 f_chiral_restr 0.0586 f_bond_d 0.0077 f_plane_restr 0.0072
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2306 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms 5
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing