1OJI

Anatomy of glycosynthesis: Structure and kinetics of the Humicola insolens Cel7B E197A and E197S glycosynthase mutants


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DYMPDB ENTRY 1DYM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7HANGING DROPS 20MM TRIS-HCL PH7-8.5, 15-30% POLYETHYLENE GLYCOL 4000, pH 7.00
Crystal Properties
Matthews coefficientSolvent content
4.169.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.312α = 90
b = 122.312β = 90
c = 82.616γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORSMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.15151000.09218.938032
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.152.2399.90.3578.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1DYM2.15105.4135580186798.10.1940.1920.226RANDOM20.97
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]
1.330.661.33-1.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.75
r_dihedral_angle_4_deg18.553
r_dihedral_angle_3_deg15.918
r_dihedral_angle_1_deg6.639
r_scangle_it3.605
r_scbond_it2.602
r_angle_refined_deg1.792
r_mcangle_it1.498
r_mcbond_it1.221
r_angle_other_deg0.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.75
r_dihedral_angle_4_deg18.553
r_dihedral_angle_3_deg15.918
r_dihedral_angle_1_deg6.639
r_scangle_it3.605
r_scbond_it2.602
r_angle_refined_deg1.792
r_mcangle_it1.498
r_mcbond_it1.221
r_angle_other_deg0.88
r_symmetry_vdw_other0.314
r_symmetry_hbond_refined0.243
r_mcbond_other0.238
r_nbd_refined0.211
r_nbd_other0.198
r_xyhbond_nbd_refined0.172
r_symmetry_vdw_refined0.113
r_chiral_restr0.102
r_nbtor_other0.09
r_bond_refined_d0.019
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms3084
Nucleic Acid Atoms
Solvent Atoms330
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing