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Crystal structure of Lactococcus lactis subsp. cremoris GH31 alpha-1,3-glucosidase in complex with glucose
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)
Crystal Properties Matthews coefficient Solvent content 3.33 63.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.362 α = 90 b = 151.362 β = 90 c = 177.263 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 2021-03-07 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 2 50 100 0.091 1 42 39.6 81029
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 100 0.947 4.7 40.3
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 2 46.617 80852 4083 99.814 0.181 0.18 0.1887 0.2081 0.2135 38.286
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] 0.855 0.427 0.855 -2.773
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.806 r_dihedral_angle_3_deg 13.637 r_dihedral_angle_4_deg 12.411 r_dihedral_angle_1_deg 7.488 r_lrange_it 6.821 r_lrange_other 6.818 r_scangle_it 6.054 r_scangle_other 6.053 r_scbond_it 4.283 r_scbond_other 4.282
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.806 r_dihedral_angle_3_deg 13.637 r_dihedral_angle_4_deg 12.411 r_dihedral_angle_1_deg 7.488 r_lrange_it 6.821 r_lrange_other 6.818 r_scangle_it 6.054 r_scangle_other 6.053 r_scbond_it 4.283 r_scbond_other 4.282 r_mcangle_it 4.086 r_mcangle_other 4.086 r_mcbond_it 3.393 r_mcbond_other 3.391 r_angle_refined_deg 1.695 r_angle_other_deg 1.417 r_symmetry_nbd_refined 0.212 r_nbd_refined 0.201 r_nbd_other 0.181 r_nbtor_refined 0.178 r_symmetry_nbd_other 0.176 r_symmetry_xyhbond_nbd_other 0.144 r_xyhbond_nbd_refined 0.141 r_symmetry_xyhbond_nbd_refined 0.12 r_chiral_restr 0.086 r_symmetry_nbtor_other 0.078 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5991 Nucleic Acid Atoms Solvent Atoms 351 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing Coot model building