☰ Navigation Tabs
Crystal Structure of Sialate O-acetylesterase from Bacteroides vulgatus by Serial Crystallography
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6NJC PDB entry 6NJC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 4.5 295 0.2 M lithium sulfate, 0.1 M acetate, pH 4.5, 2.5 M sodium chloride
Crystal Properties Matthews coefficient Solvent content 3.4 63.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.533 α = 90 b = 102.533 β = 90 c = 103.042 γ = 120
Symmetry Space Group P 65 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 295 PIXEL DECTRIS PILATUS3 6M 2018-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 Silicon nitride chips fixed target
Fixed Target Diffraction ID Description Sample Holding Support Base Motion control Details Sample Solvent 1 Silicon nitride chips Diamond/Hamburg holder GeoBrick / SmarAct
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1 10846 10846 10846
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.9 45.91 100 0.982 2.22 97.3 25754 15.29
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 99.3 0.288 0.45 6.85
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 PDB entry 6NJC 1.9 45.9 1.35 25744 1319 99.92 0.2076 0.2056 0.2053 0.2423 0.2409 23.42
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 14.3207 f_angle_d 0.7357 f_chiral_restr 0.0495 f_bond_d 0.0059 f_plane_restr 0.0039
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1587 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing MOLREP phasing