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Crystal structure of glucose bound beta-glucosidase UnBGl1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WH5
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 2.29 46.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.91 α = 90 b = 66.18 β = 90 c = 138.17 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++ 2016-05-16 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) 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 1.7 40 99.4 0.025 1 56.01 6.95 50247
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 1.7 1.8 0.997
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 1.73 37.8 47733 2513 99.4 0.12967 0.12829 0.1285 0.15576 0.1559 RANDOM 11.786
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] 0.03 0.33 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.871 r_dihedral_angle_1_deg 6.379 r_dihedral_angle_2_deg 5.517 r_long_range_B_refined 4.94 r_long_range_B_other 4.596 r_scangle_other 3.27 r_scbond_it 2.152 r_scbond_other 2.137 r_angle_refined_deg 1.903 r_mcangle_other 1.618
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.871 r_dihedral_angle_1_deg 6.379 r_dihedral_angle_2_deg 5.517 r_long_range_B_refined 4.94 r_long_range_B_other 4.596 r_scangle_other 3.27 r_scbond_it 2.152 r_scbond_other 2.137 r_angle_refined_deg 1.903 r_mcangle_other 1.618 r_mcangle_it 1.605 r_mcbond_it 1.166 r_mcbond_other 1.164 r_angle_other_deg 0.671 r_chiral_restr 0.199 r_bond_refined_d 0.012 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 3586 Nucleic Acid Atoms Solvent Atoms 558 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction PHASER phasing