☰ Navigation Tabs
The crystal structure of beta-glucosidase from the thermophilic bacterium Caldicellulosiruptor saccharolyticus in complex with beta-D-glucose determined at 1.95 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9GCI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 292.15 Co-crystals: 0.2 M magnesium chloride hexahydrate, 0.1M Bis-Tris, pH 5.5, 25% (w/v) PEG 3350 in the presence of 0.6 mM lactose
Crystal Properties Matthews coefficient Solvent content 2.52 51.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.161 α = 90 b = 98.307 β = 97.632 c = 81.776 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 2021-07-08 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 1.95 98.31 99.6 0.137 0.095 0.974 8.3 6.7 77506
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 1.95 1.99 99.9 1.655 0.634 0.653 1.8 6.7
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 1.95 62.615 77479 3968 99.508 0.173 0.1713 0.1746 0.2072 0.2106 31.517
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] -1.368 -2.456 2.266 -0.231
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.538 r_dihedral_angle_3_deg 12.115 r_dihedral_angle_1_deg 6.339 r_lrange_it 6.115 r_lrange_other 6.091 r_dihedral_angle_2_deg 6.035 r_scangle_it 4.905 r_scangle_other 4.905 r_scbond_it 3.07 r_scbond_other 3.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.538 r_dihedral_angle_3_deg 12.115 r_dihedral_angle_1_deg 6.339 r_lrange_it 6.115 r_lrange_other 6.091 r_dihedral_angle_2_deg 6.035 r_scangle_it 4.905 r_scangle_other 4.905 r_scbond_it 3.07 r_scbond_other 3.07 r_mcangle_it 2.819 r_mcangle_other 2.818 r_mcbond_it 1.916 r_mcbond_other 1.913 r_angle_refined_deg 1.197 r_angle_other_deg 0.408 r_nbd_other 0.258 r_nbd_refined 0.213 r_symmetry_nbd_refined 0.193 r_nbtor_refined 0.191 r_symmetry_nbd_other 0.187 r_xyhbond_nbd_refined 0.144 r_symmetry_xyhbond_nbd_refined 0.109 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.059 r_gen_planes_refined 0.006 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 7588 Nucleic Acid Atoms Solvent Atoms 402 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling BALBES phasing