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Crystal structure of GH5_18-E140A from Bifidobacterium longum subsp. longum ATCC 55813 in complex with Manb1-4GlcNAc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7LR1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 16% PEG 2K, 0.2 M ammonium sulfate, 0.1 M sodium citrate pH 5.6
Crystal Properties Matthews coefficient Solvent content 2.99 58.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.257 α = 90 b = 142.989 β = 90 c = 157.444 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 PILATUS 6M 2019-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 1.36242 SSRL BL9-2
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 2.3 39.36 99.9 0.996 9.1 13 105883 42.62
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 2.3 2.34 0.533
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 7LR1 2.3 39.36 1.33 104928 5139 99.07 0.1631 0.1609 0.1631 0.2059 0.2078 49.9
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 6.0793 f_angle_d 0.8861 f_chiral_restr 0.0522 f_bond_d 0.0078 f_plane_restr 0.0058
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13231 Nucleic Acid Atoms Solvent Atoms 685 Heterogen Atoms 179
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing