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Crystal structure of beta-glucosidase in rye complexed with an aglycone DIMBOA
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 4.77 74.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 194.187 α = 90 b = 194.187 β = 90 c = 194.187 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 2.5 50 99.9 0.135 30 19.3 43816
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 2.5 2.59 0.809 5.1 16.1
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 2DGA 2.5 47.1 41467 2194 99.68 0.19084 0.18991 0.1871 0.20856 0.207 RANDOM 24.632
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 34.276 r_dihedral_angle_4_deg 23.116 r_dihedral_angle_3_deg 12.716 r_scangle_it 5.902 r_dihedral_angle_1_deg 4.792 r_scbond_it 4.033 r_mcangle_it 2.652 r_angle_refined_deg 1.861 r_mcbond_it 1.509 r_chiral_restr 0.144
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.276 r_dihedral_angle_4_deg 23.116 r_dihedral_angle_3_deg 12.716 r_scangle_it 5.902 r_dihedral_angle_1_deg 4.792 r_scbond_it 4.033 r_mcangle_it 2.652 r_angle_refined_deg 1.861 r_mcbond_it 1.509 r_chiral_restr 0.144 r_bond_refined_d 0.034 r_gen_planes_refined 0.012 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 273 Heterogen Atoms 15
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling