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Crystal structure of Leuconostoc mesenteroides NRRL B-1299 N-terminally truncated dextransucrase DSR-E in orthorhombic apo-form at 1.9 angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TTO PDB ENTRY 3TTO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 285 15% PEG 3350, 0.1M ammonium nitrate, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties Matthews coefficient Solvent content 2.59 52.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.18 α = 90 b = 100.24 β = 90 c = 187.21 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 CCD ADSC QUANTUM 315r 2011-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.954 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.9 46.03 97.2 0.071 18 6.2 101840 98989 29.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.95 97 0.454 4.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 3TTO 1.9 46.03 101792 98962 4950 97.22 0.15875 0.15666 0.1626 0.19846 0.2008 RANDOM 24.25
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] -0.03 -0.01 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.352 r_dihedral_angle_4_deg 14.589 r_dihedral_angle_3_deg 11.432 r_dihedral_angle_1_deg 6.512 r_angle_refined_deg 1.835 r_angle_other_deg 1.023 r_chiral_restr 0.129 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.352 r_dihedral_angle_4_deg 14.589 r_dihedral_angle_3_deg 11.432 r_dihedral_angle_1_deg 6.512 r_angle_refined_deg 1.835 r_angle_other_deg 1.023 r_chiral_restr 0.129 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it 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 8104 Nucleic Acid Atoms Solvent Atoms 1050 Heterogen Atoms 153
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling