☰ Navigation Tabs
Structure of full-length Streptococcus mutans GtfD in complex with dextran 1000 in domain V
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9O9P 9O9P is the apo wt GtfD_FL protein structure.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 295 apo crystals of GtfD-FL in Molecular Dimensions LMB condition #44 (24% PEG 3350, 2% PEG 400, 0.05 M Hepes PH 6.8, 0.15 M NaCl) were soaked with 10 mM (final conc.) of dextran 1000 (100 mM stock soln. in water)
Crystal Properties Matthews coefficient Solvent content 2.02 39.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.841 α = 90 b = 95.485 β = 90 c = 175.326 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 EIGER X 16M 2021-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.35 84.47 97.4 0.15 0.162 0.061 0.996 6.4 6.8 58878 40.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.41 2.24 2.421 0.909 0.408 0.7 7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 2.35 64.58 1.36 52346 2577 94.77 0.2405 0.2382 0.2395 0.2842 0.2852 Random 46
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.967 f_angle_d 0.705 f_chiral_restr 0.044 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10056 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 119
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing