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GH64 family beta-1,3-glucanase from Massilia violaceinigra
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 68.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.26 α = 90 b = 126.26 β = 90 c = 71.62 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 2024-12-21 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 2.3 50 98 0.15 0.157 0.048 0.996 17 10.3 55571
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 2.3 2.42 98.9 0.701 0.736 0.223 0.942 10.5
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 2.3 47.36 27053 1425 98.07 0.16451 0.1637 0.172 0.17962 0.1868 RANDOM 27.583
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] -0.3 -0.15 -0.3 0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.448 r_dihedral_angle_3_deg 14.438 r_long_range_B_other 7.605 r_long_range_B_refined 7.591 r_dihedral_angle_1_deg 7.427 r_scangle_other 6.517 r_mcangle_it 4.831 r_mcangle_other 4.83 r_scbond_it 4.597 r_scbond_other 4.596
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.448 r_dihedral_angle_3_deg 14.438 r_long_range_B_other 7.605 r_long_range_B_refined 7.591 r_dihedral_angle_1_deg 7.427 r_scangle_other 6.517 r_mcangle_it 4.831 r_mcangle_other 4.83 r_scbond_it 4.597 r_scbond_other 4.596 r_mcbond_it 3.621 r_mcbond_other 3.572 r_angle_refined_deg 2.09 r_angle_other_deg 0.748 r_chiral_restr 0.113 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 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 199 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement SCALA data scaling iMOSFLM data reduction MOLREP phasing PDB_EXTRACT data extraction