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Crystal structure of Beta-glucosidase from Kluyveromyces marxianus in complex with glucose
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.1 293 potassium dihydrogen phosphate, PEG 8000, glycerol, glucose, pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.68 54.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 245.847 α = 90 b = 148.412 β = 112.84 c = 119.642 γ = 90
Symmetry Space Group C 1 2 1
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 ADSC QUANTUM 4r 2008-06-01 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 0.97831, 0.97928, 0.96405 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 2.54 50 100 0.089 16.6 3.8 129736 49.8
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 2.55 2.64 100 0.44 2.9 3.8
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 MAD THROUGHOUT 2.54 50 123171 6526 99.52 0.17292 0.16923 0.1648 0.24241 0.2335 RANDOM 39.7
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] -0.58 -0.12 -0.08 0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.902 r_dihedral_angle_4_deg 19.282 r_dihedral_angle_3_deg 17.846 r_dihedral_angle_1_deg 6.925 r_scangle_it 3.705 r_scbond_it 2.304 r_angle_refined_deg 1.692 r_mcangle_it 1.478 r_mcbond_it 0.787 r_chiral_restr 0.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.902 r_dihedral_angle_4_deg 19.282 r_dihedral_angle_3_deg 17.846 r_dihedral_angle_1_deg 6.925 r_scangle_it 3.705 r_scbond_it 2.304 r_angle_refined_deg 1.692 r_mcangle_it 1.478 r_mcbond_it 0.787 r_chiral_restr 0.112 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 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 26051 Nucleic Acid Atoms Solvent Atoms 1564 Heterogen Atoms 48
Software Software Software Name Purpose ADSC data collection SOLVE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling