8I5R

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


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, 24% PEG 3350, 0.1 M MES, PH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.244.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 177.738α = 90
b = 54.246β = 90
c = 83.244γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2016-03-30MSINGLE 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
11.653598.10.05532.37.395596
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)
11.651.710.9434.9

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 REPLACEMENTTHROUGHOUT5BVU1.653590849468897.970.14940.1480.1763RANDOM20.819
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]
-1.022.43-1.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.067
r_dihedral_angle_4_deg20.197
r_dihedral_angle_3_deg12.495
r_dihedral_angle_1_deg6.316
r_angle_refined_deg1.508
r_angle_other_deg0.96
r_chiral_restr0.095
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.067
r_dihedral_angle_4_deg20.197
r_dihedral_angle_3_deg12.495
r_dihedral_angle_1_deg6.316
r_angle_refined_deg1.508
r_angle_other_deg0.96
r_chiral_restr0.095
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6221
Nucleic Acid Atoms
Solvent Atoms629
Heterogen Atoms71

Software

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