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GH64 family beta-1,3-glucanase from Massilia violaceinigra in complex with a glucose disaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model SwissModel
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7 298 2.8M NaAc
Crystal Properties Matthews coefficient Solvent content 3.9 68.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.67 α = 90 b = 126.67 β = 90 c = 71.12 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 EIGER2 S 9M 2024-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.979145 SSRF BL02U1
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 1.99 41.46 100 0.2 0.359 0.081 0.996 20.1 20 44713
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 1.99 2.04 100 1.788 1 0.401 0.736 15
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 1.99 41.46 42356 2330 99.99 0.17383 0.17213 0.1827 0.20499 0.2109 RANDOM 27.094
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] -0.26 -0.13 -0.26 0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.511 r_dihedral_angle_2_deg 13.88 r_long_range_B_refined 7.125 r_dihedral_angle_1_deg 7.035 r_long_range_B_other 7.033 r_scangle_other 5.593 r_scbond_it 3.793 r_scbond_other 3.793 r_mcangle_it 3.686 r_mcangle_other 3.686
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.511 r_dihedral_angle_2_deg 13.88 r_long_range_B_refined 7.125 r_dihedral_angle_1_deg 7.035 r_long_range_B_other 7.033 r_scangle_other 5.593 r_scbond_it 3.793 r_scbond_other 3.793 r_mcangle_it 3.686 r_mcangle_other 3.686 r_mcbond_it 2.696 r_mcbond_other 2.667 r_angle_refined_deg 1.705 r_angle_other_deg 0.594 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 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 2910 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement xia2 data scaling MOLREP phasing PDB_EXTRACT data extraction Coot model building autoPROC data reduction