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Structure of beta-1,2-glucanase from Endozoicomonas elysicola (EeSGL1, ligand-free)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 potassium thiocyanate, Bis-tris propane, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.55 51.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.502 α = 90 b = 114.908 β = 90 c = 78.885 γ = 90
Symmetry Space Group P 21 21 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 6M 2018-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.4 46.442 100 0.141 0.057 0.998 14.1 13.2 40027
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 100 0.932 0.372 0.888 2.9 13.9
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 MOLECULAR REPLACEMENT FREE R-VALUE 2.4 46.442 39979 2102 99.962 0.227 0.2236 0.2269 0.2808 0.2817 45.488
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] 0.037 -0.016 -0.021
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.739 r_dihedral_angle_6_deg 14.489 r_dihedral_angle_2_deg 9.751 r_dihedral_angle_1_deg 7.397 r_lrange_it 7.332 r_lrange_other 7.332 r_scangle_it 5.432 r_scangle_other 5.432 r_mcangle_it 4.83 r_mcangle_other 4.829
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.739 r_dihedral_angle_6_deg 14.489 r_dihedral_angle_2_deg 9.751 r_dihedral_angle_1_deg 7.397 r_lrange_it 7.332 r_lrange_other 7.332 r_scangle_it 5.432 r_scangle_other 5.432 r_mcangle_it 4.83 r_mcangle_other 4.829 r_scbond_it 3.431 r_scbond_other 3.43 r_mcbond_it 3.215 r_mcbond_other 3.215 r_angle_refined_deg 1.42 r_angle_other_deg 0.504 r_symmetry_nbd_refined 0.253 r_nbd_refined 0.231 r_symmetry_nbd_other 0.208 r_nbtor_refined 0.188 r_nbd_other 0.185 r_xyhbond_nbd_refined 0.166 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.069 r_symmetry_xyhbond_nbd_other 0.023 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6729 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing