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Crystal structure of a GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei (AmGH128_I) in complex with laminaritriose
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291 8% PEG20000
8% PEGMME 550
0.1 M sodium acetate
0.2 M magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.59 52.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.758 α = 90 b = 77.98 β = 102.45 c = 46.228 γ = 90
Symmetry Space Group P 1 21 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 2016-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.239850 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 1.4 45.15 94.7 0.999 15.73 4.62 48504
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 1.4 1.49 0.672
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 1.4 36.9 46173 2335 94.72 0.1698 0.1692 0.1776 0.1817 0.1845 RANDOM 18.638
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] 0.59 0.42 -0.33 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.416 r_dihedral_angle_4_deg 17.389 r_dihedral_angle_3_deg 11.801 r_dihedral_angle_1_deg 7.144 r_mcangle_it 3.151 r_angle_other_deg 2.416 r_mcbond_it 2.323 r_mcbond_other 2.289 r_angle_refined_deg 1.803 r_chiral_restr 0.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.416 r_dihedral_angle_4_deg 17.389 r_dihedral_angle_3_deg 11.801 r_dihedral_angle_1_deg 7.144 r_mcangle_it 3.151 r_angle_other_deg 2.416 r_mcbond_it 2.323 r_mcbond_other 2.289 r_angle_refined_deg 1.803 r_chiral_restr 0.096 r_bond_other_d 0.036 r_gen_planes_other 0.024 r_bond_refined_d 0.014 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1813 Nucleic Acid Atoms Solvent Atoms 305 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing