☰ Navigation Tabs
Crystal structure of GH42 beta-galactosidase BiBga42A from Bifidobacterium longum subspecies infantis in complex with glycerol
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, HANGING DROP 293.15 0.1 M KSCN, 30% PEG MME 2000, 25% glycerol
Crystal Properties Matthews coefficient Solvent content 2.6 52.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.642 α = 90 b = 145.642 β = 90 c = 66.845 γ = 120
Symmetry Space Group P 3 2 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 CCD ADSC QUANTUM 315 2012-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.7 47.67 95.5 0.086 0.04 0.998 16.3 9.2 85479
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 63.5 0.586 0.511 0.784 1.4
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 1.7 45.91 81166 4302 95.45 0.16235 0.16108 0.1751 0.18567 0.1988 RANDOM 13.969
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] -1.34 -0.67 -1.34 4.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.181 r_dihedral_angle_2_deg 7.428 r_dihedral_angle_1_deg 6.758 r_long_range_B_refined 5.12 r_long_range_B_other 5.12 r_scangle_other 3.744 r_scbond_it 2.384 r_scbond_other 2.383 r_mcangle_it 2.165 r_mcangle_other 2.165
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.181 r_dihedral_angle_2_deg 7.428 r_dihedral_angle_1_deg 6.758 r_long_range_B_refined 5.12 r_long_range_B_other 5.12 r_scangle_other 3.744 r_scbond_it 2.384 r_scbond_other 2.383 r_mcangle_it 2.165 r_mcangle_other 2.165 r_angle_refined_deg 1.57 r_mcbond_it 1.439 r_mcbond_other 1.438 r_angle_other_deg 0.889 r_chiral_restr 0.084 r_gen_planes_other 0.017 r_gen_planes_refined 0.012 r_bond_refined_d 0.01 r_bond_other_d 0.002 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 5472 Nucleic Acid Atoms Solvent Atoms 670 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement XDS data reduction pointless data scaling MOLREP phasing