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Crystal structure of a GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei (AmGH128_I) in the complex with laminarihexaose
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 20% (w/v) Polyethylene glycol 3.350, 0.2 M Potassium Thiocyanate
Crystal Properties Matthews coefficient Solvent content 2.41 49.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.096 α = 90 b = 77.757 β = 101.99 c = 46.481 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 IMAGE PLATE RIGAKU RAXIS IV 2019-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 1.61 50 94 0.995 9.3 3 32212
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 1.61 1.71 90 0.835 1.9 2.9
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-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.61 45.47 32211 1611 94 0.187 0.227 0.2264 20.57
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] 0.53 1.319 -0.515 -0.528
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.315 r_dihedral_angle_4_deg 13.656 r_dihedral_angle_3_deg 11.975 r_dihedral_angle_1_deg 7.208 r_angle_other_deg 3.211 r_scangle_other 2.783 r_scangle_it 2.718 r_mcangle_it 2.163 r_mcangle_other 2.135 r_angle_refined_deg 2.063
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.315 r_dihedral_angle_4_deg 13.656 r_dihedral_angle_3_deg 11.975 r_dihedral_angle_1_deg 7.208 r_angle_other_deg 3.211 r_scangle_other 2.783 r_scangle_it 2.718 r_mcangle_it 2.163 r_mcangle_other 2.135 r_angle_refined_deg 2.063 r_scbond_it 1.845 r_scbond_other 1.844 r_mcbond_it 1.444 r_mcbond_other 1.359 r_nbd_other 0.24 r_nbd_refined 0.206 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.149 r_chiral_restr 0.11 r_bond_other_d 0.036 r_gen_planes_other 0.033 r_gen_planes_refined 0.016 r_bond_refined_d 0.015 r_nbtor_other 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_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1813 Nucleic Acid Atoms Solvent Atoms 262 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing