☰ Navigation Tabs
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 2.15 42.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.954 α = 90 b = 68.506 β = 95.55 c = 75.326 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 RAYONIX MX225HE HORIZONTAL FOCUSING MIRROR 2011-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90000 SPring-8 BL44XU
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 1.12 30 99.3 0.066 22.9 4.6 181100 179748 1 11.7
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 1.12 1.16 99.5 0.531 3.1 4.4 18046
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 1.12 28.2 179511 8978 98.6 0.1298 0.12869 0.1289 0.15069 0.1515 RANDOM 13.022
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] -0.75 -0.19 -0.26 0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.817 r_dihedral_angle_4_deg 13.228 r_dihedral_angle_3_deg 10.639 r_dihedral_angle_1_deg 5.928 r_scangle_it 4.007 r_scbond_it 2.772 r_mcangle_it 1.96 r_angle_refined_deg 1.407 r_rigid_bond_restr 1.346 r_mcbond_it 1.343
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.817 r_dihedral_angle_4_deg 13.228 r_dihedral_angle_3_deg 10.639 r_dihedral_angle_1_deg 5.928 r_scangle_it 4.007 r_scbond_it 2.772 r_mcangle_it 1.96 r_angle_refined_deg 1.407 r_rigid_bond_restr 1.346 r_mcbond_it 1.343 r_chiral_restr 0.098 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 3810 Nucleic Acid Atoms Solvent Atoms 627 Heterogen Atoms 35
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling