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Structure of AtBgl1A, a GH1 beta-Glucosidase from Acetivibrio thermocellus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OGZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 277.15 0.1 M HEPES pH 7.2, 10% 2-propanol, 20% PEG 4000
Crystal Properties Matthews coefficient Solvent content 3.62 66.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.27 α = 90 b = 158.27 β = 90 c = 53.962 γ = 120
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 MX300-HS 2019-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 1 NSRRC TPS 05A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.369 79.26 98.3 0.999 10.9 1.9 31219
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.37 2.46 100 0.799
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 5OGZ 2.369 79.26 31219 1638 98.25 0.175 0.1727 0.1735 0.215 0.2161 47.407
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] -1.263 -0.631 -1.263 4.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.541 r_dihedral_angle_6_deg 14.415 r_lrange_other 8.972 r_lrange_it 8.971 r_scangle_it 7.743 r_scangle_other 7.742 r_dihedral_angle_1_deg 6.977 r_dihedral_angle_2_deg 6.573 r_mcangle_it 5.485 r_mcangle_other 5.484
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.541 r_dihedral_angle_6_deg 14.415 r_lrange_other 8.972 r_lrange_it 8.971 r_scangle_it 7.743 r_scangle_other 7.742 r_dihedral_angle_1_deg 6.977 r_dihedral_angle_2_deg 6.573 r_mcangle_it 5.485 r_mcangle_other 5.484 r_scbond_it 5.162 r_scbond_other 5.161 r_mcbond_it 3.96 r_mcbond_other 3.96 r_angle_refined_deg 1.787 r_angle_other_deg 0.616 r_nbd_refined 0.227 r_nbtor_refined 0.193 r_symmetry_nbd_other 0.192 r_symmetry_xyhbond_nbd_refined 0.157 r_xyhbond_nbd_refined 0.151 r_nbd_other 0.14 r_chiral_restr 0.087 r_symmetry_nbtor_other 0.084 r_symmetry_nbd_refined 0.043 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3641 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing