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Crystal structure of a GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei (AmGH128_I)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 2.0 M sodium chloride, 0.1 M sodium acetate, pH 4.6
Crystal Properties Matthews coefficient Solvent content 1.92 35.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.877 α = 90 b = 75.378 β = 90 c = 79.148 γ = 90
Symmetry Space Group P 21 21 21
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 2019-09-17 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 1.9 50 98.2 0.985 5 3.7 17237
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 1.9 2.02 95.8 0.702 1.1 3.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.9 37.69 17235 862 98.2 0.212 0.219 0.262 0.2654 20.97
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] -0.918 -1.072 1.989
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.653 r_dihedral_angle_4_deg 16.558 r_dihedral_angle_3_deg 13.506 r_dihedral_angle_1_deg 8.027 r_angle_other_deg 2.444 r_scangle_it 2.039 r_scangle_other 2.038 r_mcangle_it 1.905 r_mcangle_other 1.905 r_angle_refined_deg 1.728
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.653 r_dihedral_angle_4_deg 16.558 r_dihedral_angle_3_deg 13.506 r_dihedral_angle_1_deg 8.027 r_angle_other_deg 2.444 r_scangle_it 2.039 r_scangle_other 2.038 r_mcangle_it 1.905 r_mcangle_other 1.905 r_angle_refined_deg 1.728 r_scbond_it 1.267 r_scbond_other 1.267 r_mcbond_other 1.148 r_mcbond_it 1.147 r_nbd_other 0.262 r_xyhbond_nbd_refined 0.208 r_nbd_refined 0.199 r_nbtor_refined 0.175 r_chiral_restr 0.074 r_bond_other_d 0.037 r_gen_planes_other 0.016 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 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 1793 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing