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Different transition state conformations for the hydrolysis of beta-mannosides and beta-glucosides in the rice Os7BGlu26 family GH1 beta-mannosidase/beta-glucosidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JHO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.25 288 0.8M K/Na tartrate, 0.1M Na HEPES, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.97 58.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.512 α = 90 b = 72.076 β = 90 c = 135.14 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 2009-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.00 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.29 30 99.9 30667 30667 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 99.7
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 4JHO 2.29 28.84 29085 1524 99.58 0.17058 0.1685 0.1689 0.20977 0.2097 RANDOM 22.354
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] -0.06 -0.43 0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.417 r_dihedral_angle_4_deg 18.03 r_dihedral_angle_3_deg 14.945 r_dihedral_angle_1_deg 5.982 r_long_range_B_refined 4.008 r_scbond_it 1.293 r_angle_refined_deg 1.274 r_mcangle_it 1.103 r_mcbond_it 0.637 r_chiral_restr 0.282
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.417 r_dihedral_angle_4_deg 18.03 r_dihedral_angle_3_deg 14.945 r_dihedral_angle_1_deg 5.982 r_long_range_B_refined 4.008 r_scbond_it 1.293 r_angle_refined_deg 1.274 r_mcangle_it 1.103 r_mcbond_it 0.637 r_chiral_restr 0.282 r_bond_refined_d 0.012 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3934 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 49
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling