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Crystal structure of Lactococcus lactis subsp. cremoris GH31 alpha-1,3-glucosidase mutant D394A in complex with nigerotriose
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 13% PEG 3350, 400 mM ammonium citrate buffer (pH 7.0), 10 mM nigerotriose
Crystal Properties Matthews coefficient Solvent content 3.37 63.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.97 α = 90 b = 151.97 β = 90 c = 177.671 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 PIXEL DECTRIS PILATUS3 S 2M 2021-06-05 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) 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 0.072 1 30.5 19.6 111675
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 1.505 0.841 2.6 20.2
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 47.948 111610 5487 99.973 0.177 0.1757 0.1858 0.1944 0.2012 35.264
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] 0.483 0.242 0.483 -1.568
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.56 r_dihedral_angle_3_deg 13.005 r_dihedral_angle_4_deg 12.221 r_dihedral_angle_1_deg 7.403 r_lrange_it 5.96 r_lrange_other 5.941 r_scangle_it 5.31 r_scangle_other 5.309 r_scbond_it 3.658 r_scbond_other 3.658
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.56 r_dihedral_angle_3_deg 13.005 r_dihedral_angle_4_deg 12.221 r_dihedral_angle_1_deg 7.403 r_lrange_it 5.96 r_lrange_other 5.941 r_scangle_it 5.31 r_scangle_other 5.309 r_scbond_it 3.658 r_scbond_other 3.658 r_mcangle_other 3.316 r_mcangle_it 3.315 r_mcbond_it 2.726 r_mcbond_other 2.721 r_angle_refined_deg 1.595 r_angle_other_deg 1.421 r_nbd_refined 0.204 r_nbd_other 0.182 r_nbtor_refined 0.178 r_symmetry_nbd_refined 0.174 r_symmetry_nbd_other 0.173 r_xyhbond_nbd_refined 0.126 r_chiral_restr 0.081 r_symmetry_nbtor_other 0.077 r_symmetry_xyhbond_nbd_refined 0.069 r_symmetry_xyhbond_nbd_other 0.03 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 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 480 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing Coot model building