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Crystal structure of a GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava (PvGH128_II)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291 ammonium sulfate 2 M
bis-tris 0.1 M
Crystal Properties Matthews coefficient Solvent content 1.93 36.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.663 α = 90 b = 33.648 β = 113.06 c = 84.259 γ = 90
Symmetry Space Group C 1 2 1
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 PILATUS 2M 2018-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.239860 LNLS W01B-MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.5 43.45 99.2 0.091 0.1 0.999 12.19 5.38 36444
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.59 98.1 0.844 0.941 0.702 1.74 5.06
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 SIRAS THROUGHOUT 1.5 40.33 34621 1823 99.33 0.17224 0.17077 0.1734 0.20034 0.2033 RANDOM 15.569
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] -0.66 0.13 1.67 -0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.255 r_dihedral_angle_4_deg 23.499 r_dihedral_angle_3_deg 12.648 r_dihedral_angle_1_deg 7.029 r_long_range_B_refined 4.072 r_long_range_B_other 3.928 r_scangle_other 1.959 r_angle_refined_deg 1.817 r_angle_other_deg 1.598 r_scbond_it 1.285
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.255 r_dihedral_angle_4_deg 23.499 r_dihedral_angle_3_deg 12.648 r_dihedral_angle_1_deg 7.029 r_long_range_B_refined 4.072 r_long_range_B_other 3.928 r_scangle_other 1.959 r_angle_refined_deg 1.817 r_angle_other_deg 1.598 r_scbond_it 1.285 r_scbond_other 1.285 r_mcangle_other 0.974 r_mcangle_it 0.973 r_mcbond_it 0.643 r_mcbond_other 0.636 r_chiral_restr 0.097 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 2091 Nucleic Acid Atoms Solvent Atoms 230 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling SHELXDE phasing