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Crystal structure of beta-glucosidase from termite Neotermes koshunensis in complex with gluconolactone
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 2.13 42.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.95 α = 90 b = 68.479 β = 95.33 c = 74.846 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 mirrors 2009-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 0.80000 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 30 98 0.057 30.7 5.5 251286 246183 1 10.1
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 1 1.04 96.1 0.888 1.9 5.5 25062
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3AHZ 1 28.2 246043 12371 97.77 0.1232 0.12221 0.142 0.139 RANDOM 12.344
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] -0.54 -0.43 0.02 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.422 r_dihedral_angle_4_deg 13.775 r_dihedral_angle_3_deg 10.649 r_dihedral_angle_1_deg 5.981 r_scangle_it 3.84 r_scbond_it 2.657 r_mcangle_it 1.866 r_angle_refined_deg 1.409 r_mcbond_it 1.281 r_rigid_bond_restr 1.272
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.422 r_dihedral_angle_4_deg 13.775 r_dihedral_angle_3_deg 10.649 r_dihedral_angle_1_deg 5.981 r_scangle_it 3.84 r_scbond_it 2.657 r_mcangle_it 1.866 r_angle_refined_deg 1.409 r_mcbond_it 1.281 r_rigid_bond_restr 1.272 r_chiral_restr 0.094 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 3819 Nucleic Acid Atoms Solvent Atoms 708 Heterogen Atoms 36
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling