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Blood Type B-converting alpha-1,3-galactosidase PpaGal from Pedobacter panaciterrae in its apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model SwissModel
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.4 293 0.2 M lithium citrate, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.84 56.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.13 α = 90 b = 129.026 β = 90.177 c = 108.296 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 EIGER X 16M 2024-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97626 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.75 107.13 96.3 0.167 0.192 0.094 0.994 6 4 73785 -3 30.94
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.797 100 0.669 0.785 0.407 0.865 2 3.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.75 107.13 73614 3647 96.175 0.253 0.251 0.2399 0.2854 0.2778 34.812
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] -1.746 -0.444 1.604 0.144
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.308 r_dihedral_angle_4_deg 23.835 r_dihedral_angle_3_deg 18.645 r_dihedral_angle_1_deg 7.688 r_lrange_it 4.902 r_lrange_other 4.901 r_angle_refined_deg 1.96 r_scangle_it 1.824 r_scangle_other 1.824 r_mcangle_it 1.706
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.308 r_dihedral_angle_4_deg 23.835 r_dihedral_angle_3_deg 18.645 r_dihedral_angle_1_deg 7.688 r_lrange_it 4.902 r_lrange_other 4.901 r_angle_refined_deg 1.96 r_scangle_it 1.824 r_scangle_other 1.824 r_mcangle_it 1.706 r_mcangle_other 1.706 r_angle_other_deg 1.46 r_scbond_it 1.04 r_scbond_other 1.04 r_mcbond_it 0.984 r_mcbond_other 0.983 r_ext_dist_refined_d 0.279 r_symmetry_xyhbond_nbd_refined 0.246 r_nbd_other 0.223 r_symmetry_nbd_refined 0.207 r_symmetry_nbd_other 0.202 r_nbd_refined 0.198 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.126 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.083 r_ncsr_local_group_6 0.067 r_ncsr_local_group_5 0.065 r_ncsr_local_group_3 0.064 r_ncsr_local_group_4 0.064 r_ncsr_local_group_1 0.062 r_ncsr_local_group_2 0.059 r_xyhbond_nbd_other 0.027 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_symmetry_xyhbond_nbd_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18556 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement Coot model building PHASER phasing XDS data scaling XDS data reduction MxCuBE data collection