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Crystal structure of sulfohexulose-1-phosphate aldolase from Paracoccus onubensis strain Merri
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-A0A418T8G4-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1 M HEPES (pH 7.5), 0.2 M L-proline, 14-18% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.88 57.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.663 α = 96.05 b = 82.485 β = 90 c = 144.77 γ = 97.42
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2023-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.5 47.98 97.7 0.11 0.077 0.991 4.9 1.8 121327
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 2.5 2.54 0.538
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 THROUGHOUT 2.5 47.88 121306 6050 97.7 0.239 0.2368 0.2299 0.2816 0.2736 RANDOM 52.59
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] -1.125 1.5217 2.6093 7.3371 2.4939 -6.2121
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.31 t_omega_torsion 2.78 t_angle_deg 0.9 t_bond_d 0.007 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20600 Nucleic Acid Atoms Solvent Atoms 484 Heterogen Atoms
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PHASER phasing