3WY6

Structure of hyperthermophilic family 12 endocellulase (E197A) from Pyrococcus furiosus in complex with laminaribiose


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP93030.12M CHES, 0.5M potassium sodium tartrate, 0.1M lithium sulfate, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 303.0K
Crystal Properties
Matthews coefficientSolvent content
2.2545.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.03α = 90
b = 118.865β = 90
c = 46.873γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2012-10-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9000SPring-8BL44XU

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
11.455095.60.0711.23.755555
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)
11.451.4890.70.3842.72565

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.4541.5555555279095.350.12810.12550.1779RANDOM16.696
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]
0.77-0.06-0.71
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free47.729
r_dihedral_angle_2_deg37.824
r_dihedral_angle_4_deg17.994
r_sphericity_bonded16.998
r_dihedral_angle_3_deg12.03
r_dihedral_angle_1_deg7.17
r_rigid_bond_restr6.158
r_angle_refined_deg2.216
r_chiral_restr0.174
r_bond_refined_d0.024
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free47.729
r_dihedral_angle_2_deg37.824
r_dihedral_angle_4_deg17.994
r_sphericity_bonded16.998
r_dihedral_angle_3_deg12.03
r_dihedral_angle_1_deg7.17
r_rigid_bond_restr6.158
r_angle_refined_deg2.216
r_chiral_restr0.174
r_bond_refined_d0.024
r_gen_planes_refined0.014
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2163
Nucleic Acid Atoms
Solvent Atoms240
Heterogen Atoms137

Software

Software
Software NamePurpose
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction