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Crystal structure of beta-glucosidase from termite Neotermes koshunensis in complex with cellobiose
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 2.17 43.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.965 α = 90 b = 68.714 β = 95.73 c = 75.832 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 ADSC QUANTUM 210r Vertically Collimating Premirror, Toroidal Focusing Mirror 2010-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL12B2 0.90000 SPring-8 BL12B2
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 1.1 30 99.9 0.064 23.4 4.9 190851 190640 1 13.8
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 1.1 1.14 100 0.508 2.4 4.8 19015
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 1.1 22.95 190485 9575 99.54 0.14829 0.14723 0.1437 0.16824 0.1641 RANDOM 15.063
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] -0.95 -0.56 -0.6 1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.178 r_dihedral_angle_4_deg 15.371 r_dihedral_angle_3_deg 11.241 r_dihedral_angle_1_deg 5.834 r_scangle_it 3.748 r_scbond_it 2.651 r_mcangle_it 1.858 r_angle_refined_deg 1.424 r_mcbond_it 1.314 r_rigid_bond_restr 1.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.178 r_dihedral_angle_4_deg 15.371 r_dihedral_angle_3_deg 11.241 r_dihedral_angle_1_deg 5.834 r_scangle_it 3.748 r_scbond_it 2.651 r_mcangle_it 1.858 r_angle_refined_deg 1.424 r_mcbond_it 1.314 r_rigid_bond_restr 1.29 r_chiral_restr 0.1 r_gen_planes_refined 0.009 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 3808 Nucleic Acid Atoms Solvent Atoms 624 Heterogen Atoms 29
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling