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Crystal structure of Levansucrase from Pseudomonas syringae in complex with a tetravalent iminosugar
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8QJ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 296 21 % PEG 8000, 0.25 M sodium acetate, 0.1 M MES pH= 6.0
Crystal Properties Matthews coefficient Solvent content 2.63 53.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.09 α = 90 b = 63.99 β = 103.496 c = 67.99 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS PILATUS 6M 2022-12-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.0000 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.65 66.1 98.6 0.08199999999999999 0.09 0.998 12.87 6.54 59642
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.69 0.97 1.052 0.741 6.67
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 (All) 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 1.65 40.003 59639 2971 98.6 0.157 0.1554 0.1554 0.187 0.1874 RANDOM 23.791
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] -0.614 -0.358 0.806 -0.018
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.758 r_dihedral_angle_3_deg 14.273 r_dihedral_angle_2_deg 8.192 r_lrange_it 6.809 r_dihedral_angle_1_deg 6.686 r_scangle_it 5.604 r_scbond_it 3.994 r_mcangle_it 3.259 r_mcbond_it 2.323 r_angle_refined_deg 1.904
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.758 r_dihedral_angle_3_deg 14.273 r_dihedral_angle_2_deg 8.192 r_lrange_it 6.809 r_dihedral_angle_1_deg 6.686 r_scangle_it 5.604 r_scbond_it 3.994 r_mcangle_it 3.259 r_mcbond_it 2.323 r_angle_refined_deg 1.904 r_nbtor_refined 0.321 r_symmetry_nbd_refined 0.222 r_nbd_refined 0.212 r_chiral_restr 0.156 r_symmetry_xyhbond_nbd_refined 0.129 r_xyhbond_nbd_refined 0.125 r_bond_refined_d 0.012 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3214 Nucleic Acid Atoms Solvent Atoms 283 Heterogen Atoms 95
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction MOLREP phasing