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Anatomy of glycosynthesis: Structure and kinetics of the Humicola insolens Cel7BE197A and E197S glycosynthase mutants
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DYM PDB ENTRY 1DYM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 HANGING DROPS 20MM TRIS-HCL PH7-8.5, 15-30% POLYETHYLENE GLYCOL 4000, pH 7.00
Crystal Properties Matthews coefficient Solvent content 2.4 47.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.282 α = 90 b = 74.83 β = 102.57 c = 86.105 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 MARRESEARCH MIRRORS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 1.5 30 99.3 0.043 24 3.5 129121
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 1.5 1.55 97.4 0.32 3.8 3.6
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 PDB ENTRY 1DYM 1.5 29.88 122540 6511 99 0.143 0.141 0.1526 0.173 0.1816 RANDOM 11.91
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] 0.14 -0.11 -0.31 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.697 r_dihedral_angle_4_deg 16.496 r_dihedral_angle_3_deg 11.849 r_dihedral_angle_1_deg 6.161 r_scangle_it 3.348 r_scbond_it 2.579 r_mcangle_it 1.634 r_angle_refined_deg 1.559 r_mcbond_it 1.435 r_angle_other_deg 0.847
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.697 r_dihedral_angle_4_deg 16.496 r_dihedral_angle_3_deg 11.849 r_dihedral_angle_1_deg 6.161 r_scangle_it 3.348 r_scbond_it 2.579 r_mcangle_it 1.634 r_angle_refined_deg 1.559 r_mcbond_it 1.435 r_angle_other_deg 0.847 r_mcbond_other 0.473 r_symmetry_vdw_other 0.232 r_symmetry_vdw_refined 0.213 r_nbd_refined 0.21 r_nbd_other 0.189 r_symmetry_hbond_refined 0.146 r_xyhbond_nbd_refined 0.109 r_chiral_restr 0.096 r_nbtor_other 0.082 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other 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 6170 Nucleic Acid Atoms Solvent Atoms 793 Heterogen Atoms 132
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing