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Ruminococcus gnavus ATC29149 endo-beta-1,4-galactosidase (RgGH98) E411A in complex with blood group A (BgA II) tetrasaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4D6C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 20% PEG 500 MME, 10% PEG20K, 0.1M pH
6.5 imidazole/MES monohydrate (acid), 30 mM sodium fluoride, 30 mM Sodium bromide and 30 mM sodium iodide
Crystal Properties Matthews coefficient Solvent content 2.43 49.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.256 α = 90 b = 103.658 β = 90 c = 113.28 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-F 2020-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.97628 Diamond I24
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 1.65 76.47 100 0.185 0.196 0.065 0.993 6.6 8.8 111311
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 1.65 1.68 99.1 3.38 3.608 1.25 0.358 8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 4D6C 1.65 76.47 105652 5529 99.94 0.1701 0.1688 0.1774 0.1952 0.2018 RANDOM 24.258
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] 0.34 -0.81 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.298 r_dihedral_angle_4_deg 17.106 r_dihedral_angle_3_deg 12.752 r_dihedral_angle_1_deg 6.984 r_angle_refined_deg 1.553 r_angle_other_deg 1.415 r_chiral_restr 0.076 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.298 r_dihedral_angle_4_deg 17.106 r_dihedral_angle_3_deg 12.752 r_dihedral_angle_1_deg 6.984 r_angle_refined_deg 1.553 r_angle_other_deg 1.415 r_chiral_restr 0.076 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6660 Nucleic Acid Atoms Solvent Atoms 693 Heterogen Atoms 122
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction Aimless data scaling MOLREP phasing