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Glycoside Hydrolase Family 157 from Labilibaculum antarcticum (LaGH157) in complex with Laminaribiose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other SeMet derivative
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1M Sodium malonate, 10% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.81 56.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 208.628 α = 90 b = 208.628 β = 90 c = 165.285 γ = 120
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 EIGER X 4M 2021-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9677 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.71 121.95 98.6 0.166 0.182 0.074 0.995 9.6 6 71618
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.71 2.77 83.1 1.894 2.086 0.86 0.375 5.6
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.71 121.95 68000 3618 98.55 0.21388 0.21083 0.2024 0.2723 0.2658 RANDOM 84.207
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] 4.19 2.1 4.19 -13.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.613 r_dihedral_angle_2_deg 8.511 r_dihedral_angle_1_deg 8.031 r_long_range_B_refined 7.492 r_long_range_B_other 7.491 r_scangle_other 2.204 r_mcangle_it 1.769 r_mcangle_other 1.769 r_angle_refined_deg 1.623 r_scbond_it 1.439
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.613 r_dihedral_angle_2_deg 8.511 r_dihedral_angle_1_deg 8.031 r_long_range_B_refined 7.492 r_long_range_B_other 7.491 r_scangle_other 2.204 r_mcangle_it 1.769 r_mcangle_other 1.769 r_angle_refined_deg 1.623 r_scbond_it 1.439 r_scbond_other 1.438 r_mcbond_it 1.054 r_mcbond_other 1.054 r_angle_other_deg 0.552 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17000 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 135
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing