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Crystal Structure of a Rice Os3BGlu6 Beta-Glucosidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CBG PDB entry 1CBG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 288 21% PEG 5000 MME, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.36 47.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.809 α = 90 b = 90.489 β = 90 c = 101.71 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC QUANTUM 315 2008-08-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0000 NSRRC BL13B1
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 1.83 30 98.9 0.095 18.99 7 46801 45193 14.892
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 1.83 1.9 96.8 0.366 4.9 6.9 4535
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1CBG 1.83 24.8 44610 44199 2347 99.08 0.16587 0.16385 0.1633 0.20423 0.2051 RANDOM 14.443
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.867 r_dihedral_angle_4_deg 19.42 r_dihedral_angle_3_deg 12.858 r_dihedral_angle_1_deg 12.806 r_scangle_it 3.134 r_scbond_it 2.07 r_angle_refined_deg 1.321 r_mcangle_it 1.254 r_mcbond_it 0.702 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.867 r_dihedral_angle_4_deg 19.42 r_dihedral_angle_3_deg 12.858 r_dihedral_angle_1_deg 12.806 r_scangle_it 3.134 r_scbond_it 2.07 r_angle_refined_deg 1.321 r_mcangle_it 1.254 r_mcbond_it 0.702 r_nbtor_refined 0.314 r_symmetry_vdw_refined 0.228 r_nbd_refined 0.203 r_symmetry_hbond_refined 0.172 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.097 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 3836 Nucleic Acid Atoms Solvent Atoms 466 Heterogen Atoms 44
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling