8I5S

Crystal structure of TxGH116 D593N acid/base mutant from Thermoanaerobacterium xylanolyticum with 2-deoxy-2-fluoroglucoside


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5BVU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52880.18 M AMMONIUM SULFATE, 22% PEG 3000, 0.1 M MES, PH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.244.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 177.192α = 90
b = 54.458β = 90
c = 83.094γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2016-03-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL15A11.0NSRRCBL15A1

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
11.453598.60.05625.85.9141041
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.451.50.7872.2

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 REPLACEMENTTHROUGHOUT5BVU1.4535134044692398.520.15660.15570.1758RANDOM18.256
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]
-0.561.27-0.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.361
r_dihedral_angle_4_deg17.58
r_dihedral_angle_3_deg11.984
r_dihedral_angle_1_deg6.358
r_angle_refined_deg1.367
r_angle_other_deg0.915
r_chiral_restr0.083
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.361
r_dihedral_angle_4_deg17.58
r_dihedral_angle_3_deg11.984
r_dihedral_angle_1_deg6.358
r_angle_refined_deg1.367
r_angle_other_deg0.915
r_chiral_restr0.083
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6221
Nucleic Acid Atoms
Solvent Atoms607
Heterogen Atoms142

Software

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