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Crystal structure of a Beta-glucosidase from Alicyclobacillus acidiphilus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 condition H3 (0.1 M Bis-Tris pH 5.5 and 25% (w/v) PEG3350) from the JCSG screen (Molecular Dimensions)
Crystal Properties Matthews coefficient Solvent content 2.86 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.654 α = 91.616 b = 91.644 β = 90.422 c = 159.342 γ = 89.988
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 6M 2019-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 0.9139 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.55 159.2743 91.1 0.098 0.996 9 84.9 367007
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.64 0.561 0.608
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE sequence 1.95 46.55 247956 24694 95.977 0.266 0.2622 0.2963 0.2588 11.898
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] -0.37 0.05 -0.046 0.268 0.119 0.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.117 r_dihedral_angle_4_deg 18.34 r_dihedral_angle_3_deg 13.714 r_dihedral_angle_1_deg 6.268 r_lrange_it 4.389 r_scangle_it 1.414 r_mcangle_it 1.387 r_angle_refined_deg 1.31 r_scbond_it 0.937 r_mcbond_it 0.891
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.117 r_dihedral_angle_4_deg 18.34 r_dihedral_angle_3_deg 13.714 r_dihedral_angle_1_deg 6.268 r_lrange_it 4.389 r_scangle_it 1.414 r_mcangle_it 1.387 r_angle_refined_deg 1.31 r_scbond_it 0.937 r_mcbond_it 0.891 r_symmetry_nbd_refined 0.339 r_metal_ion_refined 0.327 r_nbtor_refined 0.316 r_nbd_refined 0.233 r_xyhbond_nbd_refined 0.231 r_symmetry_xyhbond_nbd_refined 0.225 r_chiral_restr 0.104 r_ncsr_local_group_7 0.1 r_ncsr_local_group_13 0.093 r_ncsr_local_group_27 0.092 r_ncsr_local_group_3 0.091 r_ncsr_local_group_6 0.091 r_ncsr_local_group_28 0.09 r_ncsr_local_group_25 0.088 r_ncsr_local_group_1 0.086 r_ncsr_local_group_2 0.086 r_ncsr_local_group_4 0.086 r_ncsr_local_group_5 0.086 r_ncsr_local_group_10 0.085 r_ncsr_local_group_24 0.085 r_ncsr_local_group_18 0.084 r_ncsr_local_group_23 0.083 r_ncsr_local_group_12 0.082 r_ncsr_local_group_26 0.08 r_ncsr_local_group_21 0.078 r_ncsr_local_group_22 0.078 r_ncsr_local_group_19 0.076 r_ncsr_local_group_8 0.075 r_ncsr_local_group_9 0.075 r_ncsr_local_group_11 0.074 r_ncsr_local_group_17 0.073 r_ncsr_local_group_16 0.071 r_ncsr_local_group_15 0.069 r_ncsr_local_group_20 0.069 r_ncsr_local_group_14 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28359 Nucleic Acid Atoms Solvent Atoms 1952 Heterogen Atoms 189
Software Software Software Name Purpose REFMAC refinement XDS data reduction STARANISO data scaling BALBES phasing