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beta-glucosidase from Thermoascus aurantiacus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IID Chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M HEPES pH7.0, 0.14 M magnesium chloride, 20% 2-propanol, 0.5 mM 1-deoxynojirimycin
Crystal Properties Matthews coefficient Solvent content 2.44 49.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.945 α = 90 b = 149.752 β = 90 c = 175.529 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 100 CCD ADSC QUANTUM 210 2012-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.00000 Photon Factory BL-5A
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 2.15 50 99.8 0.129 11.6 4.17 198186
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.151 2.207 100 0.051 0.179 0.236 3.2
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 2.15 37.13 187801 9967 99.78 0.16943 0.16775 0.1746 0.2011 0.2054 RANDOM 16.499
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 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.777 r_dihedral_angle_1_deg 6.526 r_dihedral_angle_2_deg 3.373 r_long_range_B_refined 2.892 r_long_range_B_other 2.892 r_angle_refined_deg 0.921 r_mcangle_it 0.891 r_mcangle_other 0.891 r_scangle_other 0.843 r_mcbond_it 0.487
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.777 r_dihedral_angle_1_deg 6.526 r_dihedral_angle_2_deg 3.373 r_long_range_B_refined 2.892 r_long_range_B_other 2.892 r_angle_refined_deg 0.921 r_mcangle_it 0.891 r_mcangle_other 0.891 r_scangle_other 0.843 r_mcbond_it 0.487 r_mcbond_other 0.486 r_scbond_it 0.464 r_scbond_other 0.464 r_angle_other_deg 0.358 r_chiral_restr 0.048 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23908 Nucleic Acid Atoms Solvent Atoms 3232 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling SOLVE phasing