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Crystal structure of Leuconostoc citreum NRRL B-1299 dextransucrase DSR-M
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, SITTING DROP 6.5 285 20% PEG3350, 0.2M KSCN, 0.1 Pr(III)acetate, BIS-TRIS pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.78 55.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.869 α = 90 b = 128.81 β = 90 c = 234.518 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 PILATUS3 2M mirrors 2016-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8729 ESRF ID23-2
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 3.7 50 98.3 0.195 0.1 0.98 3.6 4.3 34388 44.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.7 3.9 97.3 0.528 0.284 0.822 1.4 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5lfc 3.7 50 32648 1693 98.06 0.19453 0.19234 0.195 0.23643 0.2374 RANDOM 62.15
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] -5.87 0.14 5.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.562 r_dihedral_angle_4_deg 14.208 r_dihedral_angle_3_deg 13.266 r_dihedral_angle_1_deg 5.845 r_long_range_B_refined 3.476 r_long_range_B_other 3.476 r_mcangle_it 2.267 r_mcangle_other 2.267 r_scangle_other 2.242 r_mcbond_it 1.346
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.562 r_dihedral_angle_4_deg 14.208 r_dihedral_angle_3_deg 13.266 r_dihedral_angle_1_deg 5.845 r_long_range_B_refined 3.476 r_long_range_B_other 3.476 r_mcangle_it 2.267 r_mcangle_other 2.267 r_scangle_other 2.242 r_mcbond_it 1.346 r_mcbond_other 1.346 r_scbond_it 1.288 r_scbond_other 1.288 r_angle_refined_deg 1.098 r_angle_other_deg 0.83 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 18805 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PHASER phasing XDS data reduction SCALA data scaling