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The crystal structure of beta-glucosidase from the thermophilic bacterium Caldicellulosiruptor saccharolyticus determined at 1.47 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AHX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 292.15 0.2 M magnesium chloride hexahydrate, 0.1M Bis-Tris, pH 5.5, 25% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.49 50.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.443 α = 90 b = 98.718 β = 97.487 c = 80.493 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS 12M 2019-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9763 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.47 67.86 96.5 0.068 0.06 0.997 8.6 2.5 173397 9.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.47 1.5 97.7 0.627 0.574 0.668 1.6 2.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.47 55.442 173368 8764 96.419 0.154 0.153 0.1536 0.1735 0.1739 13.622
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] -0.151 -0.276 0.717 -0.477
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.26 r_dihedral_angle_3_deg 11.909 r_dihedral_angle_2_deg 6.246 r_dihedral_angle_1_deg 6.146 r_lrange_it 4.464 r_lrange_other 4.275 r_scangle_it 3.212 r_scangle_other 3.212 r_scbond_it 2 r_scbond_other 2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.26 r_dihedral_angle_3_deg 11.909 r_dihedral_angle_2_deg 6.246 r_dihedral_angle_1_deg 6.146 r_lrange_it 4.464 r_lrange_other 4.275 r_scangle_it 3.212 r_scangle_other 3.212 r_scbond_it 2 r_scbond_other 2 r_mcangle_it 1.412 r_mcangle_other 1.412 r_angle_refined_deg 1.289 r_mcbond_it 0.916 r_mcbond_other 0.915 r_angle_other_deg 0.456 r_nbd_refined 0.22 r_symmetry_xyhbond_nbd_refined 0.217 r_symmetry_nbd_refined 0.212 r_nbd_other 0.197 r_nbtor_refined 0.192 r_symmetry_nbd_other 0.182 r_xyhbond_nbd_refined 0.14 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.069 r_gen_planes_refined 0.007 r_bond_refined_d 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7596 Nucleic Acid Atoms Solvent Atoms 829 Heterogen Atoms 111
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling BALBES phasing