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Crystal structure of hyperthermophilic beta-glucosidase from pyrococcus furiosus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1M HEPES sodium, 0.8M sodium phosphate monobasic monohydrate, 0.8M potassium phosphate monobasic, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.94 68.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.962 α = 90 b = 141.962 β = 90 c = 343.013 γ = 90
Symmetry Space Group P 43 21 2
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 RAYONIX MX-225 2009-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.9 SPring-8 BL41XU
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 2.35 50 97.9 0.092 17 7.6 145450
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 2.35 2.43 90.9 0.326 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.35 49.66 141852 7130 97.63 0.1797 0.1775 0.177 0.2226 0.2201 RANDOM 33.832
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] -0.02 -0.02 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.622 r_dihedral_angle_4_deg 21.011 r_dihedral_angle_3_deg 18.929 r_dihedral_angle_1_deg 7.033 r_scangle_it 5.043 r_scbond_it 3.198 r_angle_refined_deg 1.935 r_mcangle_it 1.818 r_mcbond_it 0.936 r_chiral_restr 0.139
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.622 r_dihedral_angle_4_deg 21.011 r_dihedral_angle_3_deg 18.929 r_dihedral_angle_1_deg 7.033 r_scangle_it 5.043 r_scbond_it 3.198 r_angle_refined_deg 1.935 r_mcangle_it 1.818 r_mcbond_it 0.936 r_chiral_restr 0.139 r_bond_refined_d 0.022 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15444 Nucleic Acid Atoms Solvent Atoms 358 Heterogen Atoms 30
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling