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Crystal structure of Lactococcus lactis subsp. cremoris GH31 alpha-1,3-glucosidase, P6322 space group
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)
Crystal Properties Matthews coefficient Solvent content 3.33 63.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.56 α = 90 b = 151.56 β = 90 c = 176.611 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 1.85 50 100 0.091 1 24.7 19.7 101843
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 1.85 1.95 100 1.144 0.882 3 18.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD FREE R-VALUE 1.85 49.659 101725 5055 99.917 0.166 0.1653 0.1761 0.1876 0.1973 32.36
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] 0.206 0.103 0.206 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.167 r_dihedral_angle_4_deg 14.825 r_dihedral_angle_3_deg 13.241 r_dihedral_angle_1_deg 7.389 r_lrange_it 6.745 r_lrange_other 6.727 r_scangle_it 6.125 r_scangle_other 6.125 r_scbond_it 4.262 r_scbond_other 4.262
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.167 r_dihedral_angle_4_deg 14.825 r_dihedral_angle_3_deg 13.241 r_dihedral_angle_1_deg 7.389 r_lrange_it 6.745 r_lrange_other 6.727 r_scangle_it 6.125 r_scangle_other 6.125 r_scbond_it 4.262 r_scbond_other 4.262 r_mcangle_other 3.651 r_mcangle_it 3.65 r_mcbond_it 2.993 r_mcbond_other 2.986 r_angle_refined_deg 1.769 r_angle_other_deg 1.487 r_nbd_other 0.238 r_symmetry_nbd_refined 0.237 r_nbd_refined 0.207 r_nbtor_refined 0.181 r_symmetry_nbd_other 0.177 r_symmetry_xyhbond_nbd_refined 0.163 r_xyhbond_nbd_refined 0.131 r_chiral_restr 0.092 r_symmetry_xyhbond_nbd_other 0.083 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 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 577 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling CRANK2 phasing Coot model building