7DKU

Crystal structure of TxGH116 E441A nucleophile mutant from Thermoanaerobacterium xylanolyticum with cellobiose


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52880.16 M AMMONIUM SULFATE, 22% PEG 3000, 0.1 M MES, PH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.2144.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 177.259α = 90
b = 54.459β = 90
c = 83.154γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2018-08-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B11.0NSRRCBL13B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.68998.20.99950.96.7105220
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)
11.61.66910.973

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 REPLACEMENTTHROUGHOUT5BVU1.688.6399857517098.140.15680.15560.1797RANDOM14.986
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]
-0.050.010.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.717
r_dihedral_angle_4_deg18.724
r_dihedral_angle_3_deg11.514
r_dihedral_angle_1_deg6.224
r_angle_refined_deg1.314
r_angle_other_deg0.914
r_chiral_restr0.079
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.717
r_dihedral_angle_4_deg18.724
r_dihedral_angle_3_deg11.514
r_dihedral_angle_1_deg6.224
r_angle_refined_deg1.314
r_angle_other_deg0.914
r_chiral_restr0.079
r_bond_refined_d0.007
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 Atoms6217
Nucleic Acid Atoms
Solvent Atoms716
Heterogen Atoms108

Software

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