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Crystal structure of beta-glucosidase in rye complexed with 2-deoxy-2-fluoroglucoside and dinitrophenol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DGA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 293 20mM HEPES, 1M LiSO4, 150mM NaCl, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.8 74.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 194.686 α = 90 b = 194.686 β = 90 c = 194.686 γ = 90
Symmetry Space Group P 41 3 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 4 2006-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 0.97800 Photon Factory BL-6A
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 2.4 58.7 100 0.104 6.7 21.6 49758
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 2.4 2.53 100 0.464 1.7 21.8 7134
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 2DGA 2.4 50 47184 2516 99.98 0.18728 0.18601 0.21172 0.1874 RANDOM 25.331
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.899 r_dihedral_angle_4_deg 19.182 r_dihedral_angle_3_deg 14.747 r_dihedral_angle_1_deg 6.656 r_scangle_it 5.031 r_scbond_it 3.619 r_mcangle_it 2.353 r_angle_refined_deg 2.055 r_mcbond_it 1.478 r_chiral_restr 0.183
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.899 r_dihedral_angle_4_deg 19.182 r_dihedral_angle_3_deg 14.747 r_dihedral_angle_1_deg 6.656 r_scangle_it 5.031 r_scbond_it 3.619 r_mcangle_it 2.353 r_angle_refined_deg 2.055 r_mcbond_it 1.478 r_chiral_restr 0.183 r_bond_refined_d 0.036 r_gen_planes_refined 0.013 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3932 Nucleic Acid Atoms Solvent Atoms 371 Heterogen Atoms 24
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling