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Crystal structure of Lactococcus lactis subsp. cremoris GH31 alpha-1,3-glucosidase mutant D394A in complex with nigerose
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 nigerose
Crystal Properties Matthews coefficient Solvent content 3.33 63.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.37 α = 90 b = 151.37 β = 90 c = 177.235 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 1.75 50 100 0.067 1 30.4 19.8 120135
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 1.75 1.84 100 1.191 0.869 2.9 20
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 1.75 47.763 120083 6004 99.984 0.167 0.1657 0.1743 0.1904 0.1989 32.269
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] 0.525 0.262 0.525 -1.702
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.028 r_dihedral_angle_4_deg 12.608 r_dihedral_angle_3_deg 12.505 r_dihedral_angle_1_deg 7.299 r_lrange_it 5.889 r_lrange_other 5.843 r_scangle_it 5.182 r_scangle_other 5.181 r_scbond_it 3.533 r_scbond_other 3.533
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.028 r_dihedral_angle_4_deg 12.608 r_dihedral_angle_3_deg 12.505 r_dihedral_angle_1_deg 7.299 r_lrange_it 5.889 r_lrange_other 5.843 r_scangle_it 5.182 r_scangle_other 5.181 r_scbond_it 3.533 r_scbond_other 3.533 r_mcangle_other 3.036 r_mcangle_it 3.035 r_mcbond_it 2.473 r_mcbond_other 2.468 r_angle_refined_deg 1.613 r_angle_other_deg 1.444 r_nbd_refined 0.204 r_nbd_other 0.191 r_nbtor_refined 0.178 r_symmetry_nbd_other 0.176 r_symmetry_nbd_refined 0.174 r_symmetry_xyhbond_nbd_refined 0.155 r_xyhbond_nbd_refined 0.124 r_chiral_restr 0.086 r_symmetry_nbtor_other 0.079 r_bond_refined_d 0.011 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 552 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing Coot model building