7W2S

Crystal structure of TxGH116 E730A mutant from Thermoanaerobacterium xylanolyticum with glucose


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2880.2 M AMMONIUM SULFATE, 22% PEG 3350, 0.1 M MES, PH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.2841.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 177.364α = 90
b = 54.708β = 90
c = 83.216γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2019-11-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B11.0NSRRCBL13B1

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
11.853099.80.11316.56.770181
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.9299.50.7220.7651.9

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 REPLACEMENTTHROUGHOUT5BVU1.853066151339899.210.15640.15450.1934RANDOM22.621
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]
-0.140.040.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.898
r_dihedral_angle_4_deg18.332
r_dihedral_angle_3_deg12.568
r_dihedral_angle_1_deg6.597
r_angle_refined_deg1.569
r_angle_other_deg0.982
r_chiral_restr0.1
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.898
r_dihedral_angle_4_deg18.332
r_dihedral_angle_3_deg12.568
r_dihedral_angle_1_deg6.597
r_angle_refined_deg1.569
r_angle_other_deg0.982
r_chiral_restr0.1
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6225
Nucleic Acid Atoms
Solvent Atoms437
Heterogen Atoms75

Software

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