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Crystal structure of inulosucrase from Lactobacillus reuteri 121 mutant R544W
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YFR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 20% PEG3000
200 mM Sodium acetate Acetic acid pH 4.5
Crystal Properties Matthews coefficient Solvent content 2.68 59.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.57 α = 90 b = 132.08 β = 110.29 c = 121.78 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 PIXEL DECTRIS PILATUS3 S 2M 2021-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17B1 0.97918 SSRF BL17B1
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 2.44 41.59 98.4 0.147 0.159 0.061 0.993 11 6.6 100399
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 2.44 2.48 82.3 0.529 0.592 0.259 0.837 4.8
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 2.44 41.59 95396 4965 98.34 0.18144 0.17964 0.1883 0.21558 0.2235 RANDOM 23.375
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] 0.21 0.04 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.932 r_dihedral_angle_4_deg 20.444 r_dihedral_angle_3_deg 14.178 r_dihedral_angle_1_deg 6.948 r_long_range_B_refined 4.633 r_long_range_B_other 4.565 r_scangle_other 3.107 r_mcangle_it 2.596 r_mcangle_other 2.596 r_scbond_it 1.923
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.932 r_dihedral_angle_4_deg 20.444 r_dihedral_angle_3_deg 14.178 r_dihedral_angle_1_deg 6.948 r_long_range_B_refined 4.633 r_long_range_B_other 4.565 r_scangle_other 3.107 r_mcangle_it 2.596 r_mcangle_other 2.596 r_scbond_it 1.923 r_scbond_other 1.923 r_mcbond_it 1.615 r_mcbond_other 1.609 r_angle_refined_deg 1.49 r_angle_other_deg 0.804 r_chiral_restr 0.084 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16338 Nucleic Acid Atoms Solvent Atoms 995 Heterogen Atoms 157
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing