6JKQ

Crystal structure of aspartate transcarbamoylase from Trypanosoma cruzi (Ligand-free form)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ML4 

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
2.2144.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.419α = 69.56
b = 79.282β = 82.9
c = 92.016γ = 63.25
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEBruker DIP-60402008-05-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.90000SPring-8BL44XU

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
12.85097.70.07415.82.444850
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)
12.82.998.40.3894.42.4

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1ML42.8129.5141411220596.440.182140.17780.26547RANDOM54.247
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]
0.6-0.140.09-0.030.12-0.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.696
r_dihedral_angle_4_deg18.056
r_dihedral_angle_3_deg17.87
r_long_range_B_refined7.363
r_long_range_B_other7.363
r_dihedral_angle_1_deg7
r_scangle_other5.233
r_mcangle_it5.069
r_mcangle_other5.069
r_mcbond_it3.223
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.696
r_dihedral_angle_4_deg18.056
r_dihedral_angle_3_deg17.87
r_long_range_B_refined7.363
r_long_range_B_other7.363
r_dihedral_angle_1_deg7
r_scangle_other5.233
r_mcangle_it5.069
r_mcangle_other5.069
r_mcbond_it3.223
r_mcbond_other3.221
r_scbond_it3.207
r_scbond_other3.206
r_angle_refined_deg1.559
r_angle_other_deg1.01
r_chiral_restr0.081
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13949
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

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