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Crystal Structure of mutant (D270A) beta-glucosidase from Listeria innocua in complex with sophorose
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 2.85 56.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.58 α = 90 b = 94.73 β = 96.29 c = 215.112 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 32.5 97.6 5.4 3.3 117573
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 32.5 111659 5914 97.46 0.2056 0.2024 0.2094 0.2674 0.2716 RANDOM 17.756
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.192 r_dihedral_angle_4_deg 20.145 r_sphericity_free 18.016 r_dihedral_angle_3_deg 14.611 r_dihedral_angle_1_deg 6.68 r_sphericity_bonded 5.976 r_rigid_bond_restr 5.493 r_angle_other_deg 2.201 r_angle_refined_deg 1.72 r_chiral_restr 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.192 r_dihedral_angle_4_deg 20.145 r_sphericity_free 18.016 r_dihedral_angle_3_deg 14.611 r_dihedral_angle_1_deg 6.68 r_sphericity_bonded 5.976 r_rigid_bond_restr 5.493 r_angle_other_deg 2.201 r_angle_refined_deg 1.72 r_chiral_restr 0.098 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_gen_planes_other 0.008 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11184 Nucleic Acid Atoms Solvent Atoms 602 Heterogen Atoms 48
Software Software Software Name Purpose MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction