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Crystal structure of Glucose bound GH1 beta-glucosidase mutant (UnBGl1_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 2.21 44.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.474 α = 90 b = 65.87 β = 90 c = 137.348 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++ 2021-08-28 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 1.78 65.87 100 0.987 8.8 7.09 45575
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 1.78 1.81 99 0.308 2.7
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 1.78 59.39 43195 2309 99.97 0.17618 0.17449 0.1827 0.20741 0.2146 RANDOM 12.922
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] -0.31 0.09 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.963 r_dihedral_angle_2_deg 7.797 r_dihedral_angle_1_deg 6.723 r_long_range_B_refined 5.602 r_long_range_B_other 5.466 r_scangle_other 3.129 r_mcangle_it 2.123 r_mcangle_other 2.123 r_scbond_it 1.954 r_scbond_other 1.953
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.963 r_dihedral_angle_2_deg 7.797 r_dihedral_angle_1_deg 6.723 r_long_range_B_refined 5.602 r_long_range_B_other 5.466 r_scangle_other 3.129 r_mcangle_it 2.123 r_mcangle_other 2.123 r_scbond_it 1.954 r_scbond_other 1.953 r_angle_refined_deg 1.505 r_mcbond_it 1.364 r_mcbond_other 1.336 r_angle_other_deg 0.516 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 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 3680 Nucleic Acid Atoms Solvent Atoms 417 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement xia2 data scaling xia2 data reduction PHASER phasing