8I5U

Crystal structure of TxGH116 D593N acid/base mutant from Thermoanaerobacterium xylanolyticum with laminaribiose


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 3350, 0.1 M MES, PH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.244.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 177.765α = 90
b = 54.129β = 90
c = 83.33γ = 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
11.450.0199.40.0440.16.7157183
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)
11.41.450.3420.9334.2

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 REPLACEMENTTHROUGHOUT5BVU1.450.01148177775498.410.1540.15320.1708RANDOM16.296
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]
-0.070.060.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.07
r_dihedral_angle_4_deg18.504
r_dihedral_angle_3_deg11.498
r_dihedral_angle_1_deg6.374
r_angle_other_deg3.623
r_angle_refined_deg1.394
r_chiral_restr0.084
r_gen_planes_other0.01
r_bond_refined_d0.008
r_gen_planes_refined0.007
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.07
r_dihedral_angle_4_deg18.504
r_dihedral_angle_3_deg11.498
r_dihedral_angle_1_deg6.374
r_angle_other_deg3.623
r_angle_refined_deg1.394
r_chiral_restr0.084
r_gen_planes_other0.01
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6221
Nucleic Acid Atoms
Solvent Atoms654
Heterogen Atoms134

Software

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