4K2M

Crystal structure of ntda from bacillus subtilis in complex with the plp external aldimine adduct with kanosamine-6-phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4K2BPDB entry 4K2B

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.62950.1M tri-sodium citrate pH 5.6, 0.2M ammonium acetate, 10-30% PEG3350, microbatch, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.5752.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.7α = 90
b = 106.44β = 96.42
c = 98.24γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDMIRRORS2011-10-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-1CLSI08ID-1

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
11.7146.899.30.06614.284108740-327.42
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.711.7598.50.7552.14

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB entry 4K2B1.7146.731.99432120108734543799.30.1540.1520.18624.2
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]
3.64993.9037-5.94022.2903
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.902
f_angle_d1.13
f_chiral_restr0.079
f_bond_d0.007
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7055
Nucleic Acid Atoms
Solvent Atoms935
Heterogen Atoms102

Software

Software
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction