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Crystal structure of Lactococcus lactis subsp. cremoris GH31 alpha-1,3-glucosidase mutant D394A in complex with nigerotetraose
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 nigerotetraose
Crystal Properties Matthews coefficient Solvent content 3.36 63.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.751 α = 90 b = 151.751 β = 90 c = 177.656 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 0.095 1 22.2 19.7 111334
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 1.068 0.882 3.3 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 47.883 111269 5471 99.953 0.167 0.1654 0.1762 0.1888 0.1974 30.183
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] 0.333 0.166 0.333 -1.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.746 r_dihedral_angle_3_deg 12.594 r_dihedral_angle_4_deg 12.404 r_dihedral_angle_1_deg 7.361 r_lrange_it 5.806 r_lrange_other 5.806 r_scangle_it 4.905 r_scangle_other 4.905 r_scbond_it 3.245 r_scbond_other 3.245
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.746 r_dihedral_angle_3_deg 12.594 r_dihedral_angle_4_deg 12.404 r_dihedral_angle_1_deg 7.361 r_lrange_it 5.806 r_lrange_other 5.806 r_scangle_it 4.905 r_scangle_other 4.905 r_scbond_it 3.245 r_scbond_other 3.245 r_mcangle_other 2.895 r_mcangle_it 2.894 r_mcbond_it 2.247 r_mcbond_other 2.24 r_angle_refined_deg 1.57 r_angle_other_deg 1.416 r_nbd_refined 0.202 r_nbd_other 0.183 r_symmetry_nbd_other 0.179 r_nbtor_refined 0.177 r_symmetry_nbd_refined 0.152 r_xyhbond_nbd_refined 0.145 r_symmetry_xyhbond_nbd_refined 0.113 r_chiral_restr 0.081 r_symmetry_nbtor_other 0.079 r_symmetry_xyhbond_nbd_other 0.039 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 638 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing Coot model building