6JKT | pdb_00006jkt

Crystal structure of aspartate transcarbamoylase from Trypanosoma cruzi in complex with N-(PHOSPHONACETYL)-L-ASPARTIC ACID (PALA).


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6JKQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.629310% PEG 3350, 0.1 M acetate buffer pH 4.6, 0.2 M ammonium acetate, 0.01 M cobalt chloride and 3% glycerol
Crystal Properties
Matthews coefficientSolvent content
2.4650.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.289α = 90
b = 157.262β = 119.77
c = 88.725γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152009-01-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.00000Photon FactoryBL-5A

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
12.35099.80.0888.63.492925
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)
12.32.381000.284.93.4

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6JKQ2.329.4488009464099.70.171120.168480.170.221450.22RANDOM22.712
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.071
r_dihedral_angle_4_deg18.394
r_dihedral_angle_3_deg15.209
r_dihedral_angle_1_deg6.151
r_scangle_it3.624
r_scbond_it2.231
r_angle_refined_deg1.481
r_mcangle_it1.208
r_mcbond_it0.61
r_chiral_restr0.166
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14629
Nucleic Acid Atoms
Solvent Atoms420
Heterogen Atoms132

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing