6JL4 | pdb_00006jl4

Crystal structure of aspartate transcarbamoylase from Trypanosoma cruzi in complex with carbamoyl aspartate (CA) and phosphate (Pi)


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, 3% glycerol
Crystal Properties
Matthews coefficientSolvent content
2.4449.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.992α = 90
b = 156.983β = 119.84
c = 88.302γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702014-01-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.00000Photon FactoryAR-NW12A

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
12.45099.90.1225.53.581396
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)
12.42.4499.80.492.23.3

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 REPLACEMENTTHROUGHOUT6JKQ2.43073258386995.080.179370.175640.180.249890.25RANDOM37.152
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]
-0.670.1-1.040.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.629
r_dihedral_angle_4_deg17.771
r_dihedral_angle_3_deg16.141
r_dihedral_angle_1_deg6.955
r_angle_refined_deg1.585
r_angle_other_deg0.826
r_chiral_restr0.081
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14687
Nucleic Acid Atoms
Solvent Atoms428
Heterogen Atoms90

Software

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