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Crystal structure of beta-glucosidase 2 from fungus Trichoderma reesei in complex with Tris
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2E3Z PDB ENTRY 2E3Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 0.1M Tris, 20-22%(w/v) PEG 3350, 0.23M MgCl2, 12.5mM sodium formate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.06 40.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.83 α = 90 b = 103.511 β = 105.37 c = 94.802 γ = 90
Symmetry Space Group P 1 21 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 315r mirrors 2009-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 1.63 30 96.9 0.088 20.9 5.6 217400 210766 1
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) 1.63 1.69 95.3 0.503 4.5 5.6 21633
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 PDB ENTRY 2E3Z 1.63 29.9 192806 10155 94.45 0.16704 0.16441 0.1756 0.21771 0.2263 RANDOM 14.638
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] 0.02 -0.23 -0.3 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.267 r_dihedral_angle_4_deg 16.729 r_dihedral_angle_3_deg 11.491 r_dihedral_angle_1_deg 4.705 r_sphericity_free 3.986 r_scangle_it 3.512 r_scbond_it 2.469 r_sphericity_bonded 2.45 r_mcangle_it 1.553 r_rigid_bond_restr 1.452
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.267 r_dihedral_angle_4_deg 16.729 r_dihedral_angle_3_deg 11.491 r_dihedral_angle_1_deg 4.705 r_sphericity_free 3.986 r_scangle_it 3.512 r_scbond_it 2.469 r_sphericity_bonded 2.45 r_mcangle_it 1.553 r_rigid_bond_restr 1.452 r_angle_refined_deg 1.439 r_mcbond_it 1.018 r_chiral_restr 0.107 r_gen_planes_refined 0.008 r_bond_refined_d 0.005 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14791 Nucleic Acid Atoms Solvent Atoms 3100 Heterogen Atoms 32
Software Software Software Name Purpose HKL-2000 data collection CNS refinement REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing