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Crystal Structure of a Rice Os3BGlu6 Beta-Glucosidase with covalently bound 2-deoxy-2-fluoroglucoside to the catalytic nucleophile E396
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GNO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 288 19% PEG 5000 MME, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.36 47.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.679 α = 90 b = 90.591 β = 90 c = 101.883 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 110 CCD ADSC QUANTUM 315 2009-01-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0000 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 30 92.9 0.045 23.9 3.7 45577 44727 18.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.81 1.87 95.1 0.184 8.7 4 4614
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3GNO 1.81 27.74 42828 2292 92.93 0.16357 0.16242 0.1607 0.18476 0.1842 RANDOM 17.078
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.836 r_dihedral_angle_4_deg 17.02 r_dihedral_angle_3_deg 13.106 r_dihedral_angle_1_deg 11.484 r_scangle_it 2.886 r_scbond_it 2.1 r_angle_refined_deg 1.28 r_mcangle_it 1.077 r_mcbond_it 0.929 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.836 r_dihedral_angle_4_deg 17.02 r_dihedral_angle_3_deg 13.106 r_dihedral_angle_1_deg 11.484 r_scangle_it 2.886 r_scbond_it 2.1 r_angle_refined_deg 1.28 r_mcangle_it 1.077 r_mcbond_it 0.929 r_nbtor_refined 0.313 r_nbd_refined 0.196 r_symmetry_vdw_refined 0.164 r_symmetry_hbond_refined 0.122 r_xyhbond_nbd_refined 0.113 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3836 Nucleic Acid Atoms Solvent Atoms 452 Heterogen Atoms 23
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling