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Structure of full-length Streptococcus mutans GtfD in complex with dextran 5000 in domain V
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9OUB 9OUB has dextran 1000 bound to domain V.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 295 Molecular Dimensions PACT condition #29:
25% PEG 1500, 0.1 M PCB buffer pH 8;
50 mM (final conc.) dextran 5000 (500 mM stock soln. in water) was added to 10.2 mg/ml GtfD-FL (168-1462) for co-crystallization
Crystal Properties Matthews coefficient Solvent content 2.61 52.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.3 α = 90 b = 94.876 β = 90 c = 182.765 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 2023-04-11 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 91.38 99.7 0.152 0.164 0.059 0.997 9.6 7.6 64523 50
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 2.393 2.561 0.903 0.458 1.1 7.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.35 63.5 64403 5802 99.35 0.2207 0.2184 0.2214 0.2669 0.2685 Random 59
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 15.845 f_angle_d 0.726 f_chiral_restr 0.05 f_bond_d 0.005 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10192 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 299
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing