4K2B

Crystal structure of ntda from bacillus subtilis in complex with the internal aldimine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OGEPDB ENTRY 2OGE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.62950.1M tri-sodium citrate, 0.2M ammonium acetate, 17.5% PEG3350, 0.4M NaCl, microbatch, temperature 295K, pH 5.6, EVAPORATION
Crystal Properties
Matthews coefficientSolvent content
2.652.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.24α = 90
b = 106.455β = 96.21
c = 98.646γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDMIRRORS2008-07-26MSINGLE 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
12.33098.40.0848.77.5451980.0528.2
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)
12.32.3885.10.2944.315.9

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 2OGE2.3128.931.354517445174232099.20.1630.1610.21432.79
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]
4.4826.4147-2.9672-1.5147
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.21
f_angle_d1.049
f_chiral_restr0.071
f_bond_d0.007
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7055
Nucleic Acid Atoms
Solvent Atoms516
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MrBUMPphasing