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Crystal structure of a GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava (PvGH128_II) in complex with laminaritriose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6UAV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291 bis-tris 0.1 M
ammonium sulfate 2 M
Crystal Properties Matthews coefficient Solvent content 1.8 31.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.432 α = 90 b = 33.871 β = 113.11 c = 84.563 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) 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 27.18 97.6 0.999 15.36 6.39 36122
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.59 0.838 2.53
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6UAV 1.5 27.18 34315 1807 97.75 0.1581 0.1562 0.1562 0.1922 0.1913 RANDOM 18.233
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] 0.57 -0.55 -0.13 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.042 r_dihedral_angle_4_deg 27.257 r_dihedral_angle_3_deg 12.933 r_dihedral_angle_1_deg 6.819 r_angle_refined_deg 1.953 r_angle_other_deg 1.59 r_chiral_restr 0.108 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.042 r_dihedral_angle_4_deg 27.257 r_dihedral_angle_3_deg 12.933 r_dihedral_angle_1_deg 6.819 r_angle_refined_deg 1.953 r_angle_other_deg 1.59 r_chiral_restr 0.108 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2096 Nucleic Acid Atoms Solvent Atoms 258 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing