☰ Navigation Tabs
Blood Type B-converting alpha-1,3-galactosidase PpaGal from Pedobacter panaciterrae in complex with D-galactose
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 = 107.011 α = 90 b = 129.025 β = 90.129 c = 108.404 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 2.978 107.011 99.4 0.21 0.234 0.103 0.989 6.4 5 60001 -3 31.6
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 2.978 3.03 99.2 0.68 0.772 0.358 0.834 2.1 4.5
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 2.98 107.011 59905 2967 99.439 0.228 0.2266 0.2166 0.2608 0.2599 36.266
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] 1.429 0.739 -2.209 0.776
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.658 r_dihedral_angle_6_deg 12.745 r_dihedral_angle_1_deg 7.427 r_dihedral_angle_2_deg 7.402 r_lrange_it 2.197 r_lrange_other 2.197 r_angle_refined_deg 1.3 r_mcangle_it 1.142 r_mcangle_other 1.142 r_scangle_it 1.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.658 r_dihedral_angle_6_deg 12.745 r_dihedral_angle_1_deg 7.427 r_dihedral_angle_2_deg 7.402 r_lrange_it 2.197 r_lrange_other 2.197 r_angle_refined_deg 1.3 r_mcangle_it 1.142 r_mcangle_other 1.142 r_scangle_it 1.067 r_scangle_other 1.067 r_mcbond_it 0.625 r_mcbond_other 0.625 r_scbond_it 0.575 r_scbond_other 0.575 r_angle_other_deg 0.458 r_nbd_other 0.223 r_symmetry_nbd_refined 0.21 r_symmetry_nbd_other 0.206 r_nbd_refined 0.186 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.13 r_symmetry_xyhbond_nbd_refined 0.099 r_symmetry_nbtor_other 0.083 r_ncsr_local_group_2 0.063 r_chiral_restr 0.06 r_ncsr_local_group_3 0.06 r_ncsr_local_group_1 0.056 r_ncsr_local_group_6 0.056 r_ncsr_local_group_4 0.055 r_ncsr_local_group_5 0.053 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18556 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement Coot model building PHASER phasing XDS data scaling XDS data reduction MxCuBE data collection