3TW6 | pdb_00003tw6

Structure of Rhizobium etli pyruvate carboxylase T882A with the allosteric activator, acetyl coenzyme-A


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829814% PEG 4000, 10% MPD, 0.45M potassium chloride, 0.1 M triethanolamine, 1 mM TCEP, 5 mM ADP, 5 mM phosphonoacetate, 1 mM acetyl-CoA, 10 mM magnesium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.0960.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 370.445α = 90
b = 91.55β = 134.71
c = 261.354γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDADSC QUANTUM 3152009-07-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.979APS19-ID

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
12.45099.20.08319.33.6243161241087-3
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)
12.42.49970.3513.43.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.446.432289491213398.730.19170.18940.18930.235310.2346RANDOM44.238
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]
-0.48-0.210.88-0.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.556
r_dihedral_angle_4_deg17.911
r_dihedral_angle_3_deg17.188
r_dihedral_angle_1_deg7.264
r_angle_refined_deg2.026
r_chiral_restr0.129
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms31746
Nucleic Acid Atoms
Solvent Atoms793
Heterogen Atoms215

Software

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