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Crystal structure of mutant (D270A) beta-glucosidase from Listeria innocua in complex with gentiobiose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZOE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 PEG 4000, NaCl, LiSO4, glycerol
Crystal Properties Matthews coefficient Solvent content 2.86 56.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.6 α = 90 b = 95.16 β = 96.38 c = 215.404 γ = 90
Symmetry Space Group I 1 2 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 CCD ADSC QUANTUM 210 2014-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 32.51 92.4 4.7 3 112030
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 4ZOE 2 32.51 106407 5633 92.32 0.1664 0.1627 0.1726 0.2354 0.2403 RANDOM 17.435
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] -0.01 0.03 -0.02 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.823 r_sphericity_free 19.629 r_dihedral_angle_4_deg 19.557 r_dihedral_angle_3_deg 14.573 r_dihedral_angle_1_deg 6.863 r_sphericity_bonded 6.136 r_rigid_bond_restr 4.627 r_angle_refined_deg 1.832 r_angle_other_deg 1.274 r_chiral_restr 0.106
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.823 r_sphericity_free 19.629 r_dihedral_angle_4_deg 19.557 r_dihedral_angle_3_deg 14.573 r_dihedral_angle_1_deg 6.863 r_sphericity_bonded 6.136 r_rigid_bond_restr 4.627 r_angle_refined_deg 1.832 r_angle_other_deg 1.274 r_chiral_restr 0.106 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11184 Nucleic Acid Atoms Solvent Atoms 807 Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement MOLREP phasing PDB_EXTRACT data extraction