☰ Navigation Tabs
Crystal structure of Leuconostoc citreum NRRL B-1299 N-terminally truncated dextransucrase DSR-M in complex with isomaltotetraose
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 6.5 295 PEG 3350 20 %, 0.2 M Sodium citrate tribasic dihydrate, 0.1 M Bis-Tris propane 6.5
Crystal Properties Matthews coefficient Solvent content 4.98 75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 185.308 α = 90 b = 185.308 β = 90 c = 150.774 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 PILATUS 6M 2016-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9762 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 3.9 47.96 97.3 13.5 4.7 26662
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.9 4.11
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 3.9 47.96 25343 1319 96.44 0.21125 0.21015 0.23209 0.1938 RANDOM 115.304
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] 0.11 0.06 0.11 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.46 r_long_range_B_refined 15.766 r_long_range_B_other 15.763 r_dihedral_angle_3_deg 13.679 r_dihedral_angle_4_deg 12.564 r_scangle_other 10.938 r_mcangle_it 10.025 r_mcangle_other 10.024 r_scbond_it 6.981 r_scbond_other 6.981
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.46 r_long_range_B_refined 15.766 r_long_range_B_other 15.763 r_dihedral_angle_3_deg 13.679 r_dihedral_angle_4_deg 12.564 r_scangle_other 10.938 r_mcangle_it 10.025 r_mcangle_other 10.024 r_scbond_it 6.981 r_scbond_other 6.981 r_dihedral_angle_1_deg 6.785 r_mcbond_it 6.463 r_mcbond_other 6.457 r_angle_refined_deg 1.369 r_angle_other_deg 0.954 r_chiral_restr 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 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 8362 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing