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Structure of beta-glucosidase A from Paenibacillus polymyxa complexed with multivalent inhibitors.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E4I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 13% (v/v) PEG 3350, 0.2M sodium nitrate, 3% 2-Methyl-2,4-pentanediol (MPD) and 0.1 M BisTris propane, pH 7.5 and 0.56 mM 6-Cyclohexylhexyl beta-D-maltoside.
Cryoprotectant mother liquor supplemented with 25% glycerol.
Crystal Properties Matthews coefficient Solvent content 3.64 66.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.096 α = 90 b = 146.096 β = 90 c = 140.345 γ = 90
Symmetry Space Group P 4 21 2
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 PILATUS3 S 6M KB focusing mirrors 2018-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979260 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.85 48.7 76.4 0.141 0.151 0.052 0.985 10.3 7.8 27295 45.005
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.85 3 79.1 0.689 0.737 0.252 0.804 2.8 7.7
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1E4I 2.85 48.52 25865 1405 75.55 0.18315 0.18056 0.1865 0.23128 0.2373 RANDOM 43.586
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] -0.42 -0.42 0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.087 r_dihedral_angle_4_deg 21.54 r_dihedral_angle_3_deg 16.423 r_long_range_B_refined 6.566 r_long_range_B_other 6.562 r_dihedral_angle_1_deg 6.426 r_scangle_other 4.292 r_mcangle_it 3.911 r_mcangle_other 3.911 r_scbond_it 2.622
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.087 r_dihedral_angle_4_deg 21.54 r_dihedral_angle_3_deg 16.423 r_long_range_B_refined 6.566 r_long_range_B_other 6.562 r_dihedral_angle_1_deg 6.426 r_scangle_other 4.292 r_mcangle_it 3.911 r_mcangle_other 3.911 r_scbond_it 2.622 r_scbond_other 2.622 r_mcbond_it 2.486 r_mcbond_other 2.472 r_angle_refined_deg 1.381 r_angle_other_deg 1.259 r_chiral_restr 0.058 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7294 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing