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Archaeal oligosaccharyltransferase AglB from Archaeoglobus fulgidus in complex with an inhibitory peptide and a dolichol-phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GMY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 6 293 50 mM NaCl, 0.1 M Na-citrate, pH 6.0, 18-22 % PEG400
Crystal Properties Matthews coefficient Solvent content 2.66 53.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 345.74 α = 90 b = 48.69 β = 90 c = 63.56 γ = 90
Symmetry Space Group P 21 21 2
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 9M micro-focused beam of 10 micro m x 15 micro m (horizontal x vertical) 2019-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.0000 SPring-8 BL32XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.7 49.4 100 0.432 0.435 0.998 13.6 79.5 30677 70.16
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.8 99.9 8.718 8.776 0.756 1.3 76.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5GMY 2.7 24.84 1.35 30599 1485 99.75 0.2171 0.2152 0.2161 0.2522 0.2505 79
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 17.4423 f_angle_d 0.5916 f_chiral_restr 0.0475 f_plane_restr 0.0047 f_bond_d 0.0028
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7032 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 185
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX phasing PHENIX refinement Coot model building