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Crystal structure of Leuconostoc citreum NRRL B-1299 N-terminally truncated dextransucrase DSR-M in complex with sucrose
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 285 0.2 M Sodium citrate tribasic dihydrate 0.1 M Bis-Tris propane 6.5 20 % w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 4.96 75.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.625 α = 90 b = 183.625 β = 90 c = 146.804 γ = 120
Symmetry Space Group P 31 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 PILATUS3 S 6M 2016-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.97625 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.6 50 98.4 4.9 3.9 32876
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 3.6 50 31258 1608 98.15 0.19996 0.19849 0.2022 0.2282 0.2321 RANDOM 90.249
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] -2.58 -1.29 -2.58 8.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.863 r_dihedral_angle_4_deg 16.678 r_dihedral_angle_3_deg 14.551 r_dihedral_angle_1_deg 6.389 r_long_range_B_refined 5.555 r_long_range_B_other 5.554 r_scangle_other 3.983 r_mcangle_it 3.531 r_mcangle_other 3.53 r_scbond_it 2.431
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.863 r_dihedral_angle_4_deg 16.678 r_dihedral_angle_3_deg 14.551 r_dihedral_angle_1_deg 6.389 r_long_range_B_refined 5.555 r_long_range_B_other 5.554 r_scangle_other 3.983 r_mcangle_it 3.531 r_mcangle_other 3.53 r_scbond_it 2.431 r_scbond_other 2.43 r_mcbond_it 2.17 r_mcbond_other 2.17 r_angle_refined_deg 1.263 r_angle_other_deg 0.747 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 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 8588 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling