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Crystal structure of the glycosynthase mutant D324N of Escherichia coli GH63 glycosidase in complex with glucose and lactose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3W7T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 20% PEG 8000, 0.4 M magnesium chloride, 100 mM Tris-HCl buffer, pH 6.0
Crystal Properties Matthews coefficient Solvent content 1.83 32.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.423 α = 90 b = 136.911 β = 100.72 c = 81.518 γ = 90
Symmetry Space Group P 1 21 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 2010-11-08 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) R Merge I (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 1.8 50 96.8 0.05 32.3 3.4 110133
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.86 90.8 0.197 7.2 3.2
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 3W7T 1.8 31.12 104563 5521 96.51 0.15091 0.14899 0.1576 0.187 0.1954 RANDOM 15.734
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 35.319 r_dihedral_angle_4_deg 15.37 r_dihedral_angle_3_deg 12.171 r_dihedral_angle_1_deg 6.044 r_angle_other_deg 3.691 r_angle_refined_deg 1.183 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_other 0.007 r_gen_planes_refined 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.319 r_dihedral_angle_4_deg 15.37 r_dihedral_angle_3_deg 12.171 r_dihedral_angle_1_deg 6.044 r_angle_other_deg 3.691 r_angle_refined_deg 1.183 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_other 0.007 r_gen_planes_refined 0.005 r_bond_other_d 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12125 Nucleic Acid Atoms Solvent Atoms 1286 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement Coot model building HKL-2000 data scaling MOLREP phasing