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Structure of the A type blood alpha-D-galactosamine galactosaminidase from Flavonifractor plautii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 292 0.1 M BICINE pH 9, 20% w/v PEG 6000
Crystal Properties Matthews coefficient Solvent content 3.02 59.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.685 α = 90 b = 164.568 β = 90.3 c = 131.645 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 PILATUS3 S 6M 2022-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 1.1806 CLSI 08B1-1
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 2 39.44 98.9 0.063 0.075 0.04 0.998 13.6 3.4 290235
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 2 2.03 98.7 1.244 1.472 0.781 0.403 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2 39.44 275678 14518 98.71 0.169 0.16772 0.1765 0.1933 0.2008 RANDOM 33.934
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] -0.2 0.07 0.32 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.853 r_dihedral_angle_2_deg 9.314 r_dihedral_angle_1_deg 6.771 r_long_range_B_refined 5.647 r_long_range_B_other 5.645 r_scangle_other 3.664 r_scbond_it 2.472 r_scbond_other 2.441 r_mcangle_it 2.141 r_mcangle_other 2.141
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.853 r_dihedral_angle_2_deg 9.314 r_dihedral_angle_1_deg 6.771 r_long_range_B_refined 5.647 r_long_range_B_other 5.645 r_scangle_other 3.664 r_scbond_it 2.472 r_scbond_other 2.441 r_mcangle_it 2.141 r_mcangle_other 2.141 r_mcbond_it 1.527 r_mcbond_other 1.527 r_angle_refined_deg 1.465 r_angle_other_deg 0.516 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 25335 Nucleic Acid Atoms Solvent Atoms 3337 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing