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Crystal structure of beta-glucosidase from termite Neotermes koshunensis in complex with a new glucopyranosidic product
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AHZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 0.1M Bis-Tris, 18-21% (w/v) PEG 3350, 0.1-0.25M MgCl2, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.14 42.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.785 α = 90 b = 68.5 β = 95.38 c = 75.075 γ = 90
Symmetry Space Group C 1 2 1
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 MARMOSAIC 300 mm CCD Vertically Focusing Mirror 2011-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13C1 0.97622 NSRRC BL13C1
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 1.28 30 99.7 0.036 39.3 3.8 120278 119961 1 15.3
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 1.28 1.33 99.8 0.197 8.3 3.8 11983
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 3AHZ 1.28 22.9 119863 6025 99.47 0.12162 0.12045 0.1185 0.14383 0.1421 RANDOM 13.15
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] -0.78 -0.44 -0.03 0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.095 r_dihedral_angle_4_deg 15.05 r_dihedral_angle_3_deg 10.695 r_dihedral_angle_1_deg 5.852 r_scangle_it 3.994 r_scbond_it 2.74 r_mcangle_it 1.88 r_angle_refined_deg 1.399 r_mcbond_it 1.246 r_rigid_bond_restr 1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.095 r_dihedral_angle_4_deg 15.05 r_dihedral_angle_3_deg 10.695 r_dihedral_angle_1_deg 5.852 r_scangle_it 3.994 r_scbond_it 2.74 r_mcangle_it 1.88 r_angle_refined_deg 1.399 r_mcbond_it 1.246 r_rigid_bond_restr 1.24 r_chiral_restr 0.096 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3810 Nucleic Acid Atoms Solvent Atoms 640 Heterogen Atoms 62
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling