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N-terminally truncated dextransucrase DSR-E from Leuconostoc mesenteroides NRRL B-1299 in complex with D-glucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TTQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 285 20% PEG 3350, 0.1 M ammonium nitrate
Crystal Properties Matthews coefficient Solvent content 2.46 49.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.77 α = 90 b = 98.98 β = 90 c = 181.91 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 PSI PILATUS 6M 2012-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97625 ESRF ID29
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 2.3 47.75 99.5 0.099 13.7 6.5 54664
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.36 94.2 0.65 2.1 4.6
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 3TTQ 2.3 47.7 51888 2772 99.54 0.17155 0.16873 0.22332 0.2046 RANDOM 39.772
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] -0.02 -0.04 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.499 r_dihedral_angle_4_deg 13.924 r_dihedral_angle_3_deg 11.409 r_long_range_B_refined 7.243 r_long_range_B_other 7.243 r_dihedral_angle_1_deg 6.396 r_scangle_other 5.212 r_mcangle_it 4.114 r_mcangle_other 4.114 r_scbond_it 3.399
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.499 r_dihedral_angle_4_deg 13.924 r_dihedral_angle_3_deg 11.409 r_long_range_B_refined 7.243 r_long_range_B_other 7.243 r_dihedral_angle_1_deg 6.396 r_scangle_other 5.212 r_mcangle_it 4.114 r_mcangle_other 4.114 r_scbond_it 3.399 r_scbond_other 3.398 r_mcbond_it 2.758 r_mcbond_other 2.757 r_angle_refined_deg 1.531 r_angle_other_deg 0.856 r_chiral_restr 0.099 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.004 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 8100 Nucleic Acid Atoms Solvent Atoms 395 Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing