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Crystal structure of Lactococcus lactis subsp. cremoris GH31 alpha-1,3-glucosidase mutant D394A in complex with kojibiose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7WJA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 14% PEG 3350, 400 mM ammonium citrate buffer (pH 7.0), 10 mM kojibiose
Crystal Properties Matthews coefficient Solvent content 3.35 63.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.718 α = 90 b = 151.718 β = 90 c = 177.681 γ = 120
Symmetry Space Group P 63 2 2
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 270 2021-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 50 100 0.09 1 25 19.7 111324
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 100 1.235 0.848 2.8 18.9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7WJA 1.8 44.46 111247 5468 99.96 0.171 0.1698 0.1797 0.1907 0.1988 30.748
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] 0.301 0.15 0.301 -0.976
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.593 r_dihedral_angle_3_deg 12.81 r_dihedral_angle_4_deg 12.488 r_dihedral_angle_1_deg 7.311 r_lrange_it 5.899 r_lrange_other 5.854 r_scangle_it 5.032 r_scangle_other 5.031 r_scbond_it 3.34 r_scbond_other 3.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.593 r_dihedral_angle_3_deg 12.81 r_dihedral_angle_4_deg 12.488 r_dihedral_angle_1_deg 7.311 r_lrange_it 5.899 r_lrange_other 5.854 r_scangle_it 5.032 r_scangle_other 5.031 r_scbond_it 3.34 r_scbond_other 3.34 r_mcangle_other 3.086 r_mcangle_it 3.085 r_mcbond_it 2.406 r_mcbond_other 2.4 r_angle_refined_deg 1.563 r_angle_other_deg 1.42 r_nbd_refined 0.202 r_nbd_other 0.2 r_symmetry_nbd_refined 0.181 r_nbtor_refined 0.178 r_symmetry_nbd_other 0.173 r_symmetry_xyhbond_nbd_refined 0.166 r_xyhbond_nbd_refined 0.13 r_chiral_restr 0.081 r_symmetry_nbtor_other 0.077 r_symmetry_xyhbond_nbd_other 0.041 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5988 Nucleic Acid Atoms Solvent Atoms 580 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing Coot model building