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Ruminococcus gnavus ATC29149 endo-beta-1,4-galactosidase (RgGH98) in complex with blood group A trisaccharide
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 293 12.5% MPD; 25% PEG 1000; 12.5% PEG 3350, 0.1 M Sodium HEPES/MOPS pH 7.5, 30 mM
magnesium chloride hexahydrate and 30 mM calcium chloride dihydrate
Crystal Properties Matthews coefficient Solvent content 2.68 54.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.594 α = 90 b = 86.95 β = 100.33 c = 110.196 γ = 90
Symmetry Space Group P 1 21 1
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 2018-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.99990 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 1.95 108.411 99.9 0.15 0.172 0.069 0.988 5.8 5.4 145680
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 1.95 1.98 97.7 1.748 1.931 0.808 0.394 1.1 5.4
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 1.95 108.41 137854 7379 99.71 0.1866 0.18487 0.192 0.21883 0.2245 RANDOM 42.812
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] -1.75 1.25 0.59 0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.125 r_dihedral_angle_4_deg 16.322 r_dihedral_angle_3_deg 12.663 r_long_range_B_refined 6.419 r_long_range_B_other 6.411 r_dihedral_angle_1_deg 6.331 r_scangle_other 2.733 r_mcangle_it 1.777 r_mcangle_other 1.777 r_scbond_it 1.711
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.125 r_dihedral_angle_4_deg 16.322 r_dihedral_angle_3_deg 12.663 r_long_range_B_refined 6.419 r_long_range_B_other 6.411 r_dihedral_angle_1_deg 6.331 r_scangle_other 2.733 r_mcangle_it 1.777 r_mcangle_other 1.777 r_scbond_it 1.711 r_scbond_other 1.711 r_angle_refined_deg 1.289 r_mcbond_it 1.13 r_mcbond_other 1.13 r_angle_other_deg 1.037 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13342 Nucleic Acid Atoms Solvent Atoms 823 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing