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Crystal structure of beta-glucosidase from Acetivibrio thermocellus
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, HANGING DROP 7.5 295 0.1M HEPES, 55% MPD
Crystal Properties Matthews coefficient Solvent content 3.86 68.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.93 α = 60.118 b = 158.62 β = 88.192 c = 158.91 γ = 87.478
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2019-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54179
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 3 35 93.9 0.165 0.233 0.97 4.33 1.99 175099
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.2 0.65 0.92 0.5
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 3 34.991 175099 8755 94.062 0.335 0.3 0.3115 0.35 0.3206 39.256
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] 0.036 0.023 0.014 -0.008 0.008 -0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.756 r_dihedral_angle_4_deg 20.401 r_dihedral_angle_3_deg 16.489 r_dihedral_angle_1_deg 7.467 r_lrange_other 6.738 r_lrange_it 6.737 r_mcangle_it 3.631 r_mcangle_other 3.631 r_scangle_it 2.757 r_scangle_other 2.756
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.756 r_dihedral_angle_4_deg 20.401 r_dihedral_angle_3_deg 16.489 r_dihedral_angle_1_deg 7.467 r_lrange_other 6.738 r_lrange_it 6.737 r_mcangle_it 3.631 r_mcangle_other 3.631 r_scangle_it 2.757 r_scangle_other 2.756 r_mcbond_it 2.154 r_mcbond_other 2.153 r_scbond_it 1.554 r_scbond_other 1.553 r_angle_refined_deg 1.407 r_angle_other_deg 1.142 r_nbd_other 0.3 r_symmetry_nbd_refined 0.241 r_nbd_refined 0.23 r_xyhbond_nbd_refined 0.23 r_symmetry_nbd_other 0.222 r_symmetry_xyhbond_nbd_refined 0.221 r_nbtor_refined 0.17 r_symmetry_xyhbond_nbd_other 0.085 r_xyhbond_nbd_other 0.079 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.053 r_bond_refined_d 0.005 r_bond_other_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 43908 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing