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High resolution crystal strucutre of highly glucose tolerant GH1 beta-glucosidase (UnBGl1_C188V_H261W)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9J3W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.2 295 0.056M Sodium phosphate monobasic monohydrate, 1.344M Potassium phosphate dibasic, pH 8.2
Crystal Properties Matthews coefficient Solvent content 2.24 45.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.75 α = 90 b = 66.38 β = 90 c = 137.49 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 CCD RAYONIX MX225HE 2023-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.97777 RRCAT INDUS-2 PX-BL21
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.55 30 99.7 0.1 0.998 14.42 743 69348
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.65 0.827 0.767 2.45 6.17
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 1.55 29.89 65880 3468 99.65 0.14 0.13881 0.1386 0.16302 0.1629 RANDOM 11.335
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] 0.09 -0.16 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.265 r_dihedral_angle_2_deg 9.391 r_dihedral_angle_1_deg 6.381 r_long_range_B_refined 5.241 r_long_range_B_other 4.808 r_scangle_other 3.545 r_scbond_it 2.32 r_scbond_other 2.32 r_mcangle_other 1.848 r_mcangle_it 1.847
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.265 r_dihedral_angle_2_deg 9.391 r_dihedral_angle_1_deg 6.381 r_long_range_B_refined 5.241 r_long_range_B_other 4.808 r_scangle_other 3.545 r_scbond_it 2.32 r_scbond_other 2.32 r_mcangle_other 1.848 r_mcangle_it 1.847 r_angle_refined_deg 1.679 r_mcbond_it 1.277 r_mcbond_other 1.246 r_angle_other_deg 0.594 r_chiral_restr 0.089 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 3681 Nucleic Acid Atoms Solvent Atoms 523 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction PHASER phasing