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Crystal structure of beta-glucosidase from termite Neotermes koshunensis in complex with salicin
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 2.16 42.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.908 α = 90 b = 68.536 β = 95.7 c = 75.663 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 315r Vertically Focusing Mirror 2010-06-22 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 1.15 30 99.4 0.046 34.5 4.7 167114 166145 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 1.15 1.19 99.7 0.458 3.7 4.5 16643
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 1.15 25.2 165967 8352 99.3 0.12937 0.12807 0.1279 0.15428 0.1544 RANDOM 15.59
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] -1.03 -0.46 -0.17 1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.841 r_dihedral_angle_4_deg 15.271 r_dihedral_angle_3_deg 10.661 r_dihedral_angle_1_deg 5.94 r_scangle_it 4.21 r_scbond_it 2.963 r_mcangle_it 1.985 r_angle_refined_deg 1.431 r_rigid_bond_restr 1.422 r_mcbond_it 1.379
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.841 r_dihedral_angle_4_deg 15.271 r_dihedral_angle_3_deg 10.661 r_dihedral_angle_1_deg 5.94 r_scangle_it 4.21 r_scbond_it 2.963 r_mcangle_it 1.985 r_angle_refined_deg 1.431 r_rigid_bond_restr 1.422 r_mcbond_it 1.379 r_chiral_restr 0.099 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 669 Heterogen Atoms 36
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling