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Crystal Structure of Truncated Alternansucrase from Leuconostoc mesenteroides NRRL B-1355
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LFC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 285 PEG3350 14%
0.4M NaNO3
Crystal Properties Matthews coefficient Solvent content 2.53 51.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.235 α = 90 b = 134.804 β = 90 c = 237.035 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 x-ray 100 PIXEL DECTRIS EIGER X 4M 2017-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.8 47.82 99.4 0.088 7.3 6.9 80120 60.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.95 99.9 0.571 0.87 1.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5LFC 2.8 47.82 76019 4021 99.31 0.2082 0.20665 0.23732 0.2186 RANDOM 65.53
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] -0.31 -1.57 1.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.345 r_dihedral_angle_4_deg 18.177 r_dihedral_angle_3_deg 14.613 r_long_range_B_refined 7.61 r_long_range_B_other 7.609 r_dihedral_angle_1_deg 5.622 r_scangle_other 4.437 r_mcangle_it 4.403 r_mcangle_other 4.403 r_scbond_it 2.777
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.345 r_dihedral_angle_4_deg 18.177 r_dihedral_angle_3_deg 14.613 r_long_range_B_refined 7.61 r_long_range_B_other 7.609 r_dihedral_angle_1_deg 5.622 r_scangle_other 4.437 r_mcangle_it 4.403 r_mcangle_other 4.403 r_scbond_it 2.777 r_scbond_other 2.776 r_mcbond_it 2.758 r_mcbond_other 2.756 r_angle_refined_deg 1.265 r_angle_other_deg 1.078 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.005 r_gen_planes_other 0.005 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 19193 Nucleic Acid Atoms Solvent Atoms 278 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing