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Crystal structure of glucose bound covalent intermediate of GH1 beta-glucosidase (UnBGl1)
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 45.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.2 α = 90 b = 65.8 β = 90 c = 137.9 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++ 2019-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 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 2 30 98.8 0.907 6.95 3.7 31988
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 2 2.1 97.6 0.562 2.04
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 2 29.69 30390 1600 99.06 0.18792 0.18563 0.1946 0.23157 0.2413 RANDOM 29.731
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] 0.55 1.23 -1.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.013 r_dihedral_angle_2_deg 7.239 r_dihedral_angle_1_deg 6.869 r_long_range_B_refined 5.81 r_long_range_B_other 5.809 r_scangle_other 4.083 r_mcangle_it 2.986 r_mcangle_other 2.986 r_scbond_it 2.809 r_scbond_other 2.801
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.013 r_dihedral_angle_2_deg 7.239 r_dihedral_angle_1_deg 6.869 r_long_range_B_refined 5.81 r_long_range_B_other 5.809 r_scangle_other 4.083 r_mcangle_it 2.986 r_mcangle_other 2.986 r_scbond_it 2.809 r_scbond_other 2.801 r_mcbond_it 2.192 r_mcbond_other 2.192 r_angle_refined_deg 1.549 r_angle_other_deg 0.541 r_chiral_restr 0.073 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 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 3564 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing