3E0K

Crystal structure of C-termianl domain of N-acetylglutamate synthase from Vibrio parahaemolyticus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52891.0 M Ammonium sulfate, 0.1 M Bis-Tris pH 5.5, 1% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
3.3663.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.232α = 90
b = 64.232β = 90
c = 112.718γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-04-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97921APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.525098.30.0860.3172.439.385098366-367.7
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)
12.522.541000.872.439.7197

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.52508351835138998.620.216840.216840.215120.25447RANDOM45.146
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]
0.830.83-1.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.382
r_dihedral_angle_3_deg17.776
r_dihedral_angle_4_deg15.55
r_dihedral_angle_1_deg5.948
r_scangle_it2.091
r_scbond_it1.425
r_angle_refined_deg1.413
r_mcangle_it1.11
r_mcbond_it0.64
r_nbtor_refined0.313
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.382
r_dihedral_angle_3_deg17.776
r_dihedral_angle_4_deg15.55
r_dihedral_angle_1_deg5.948
r_scangle_it2.091
r_scbond_it1.425
r_angle_refined_deg1.413
r_mcangle_it1.11
r_mcbond_it0.64
r_nbtor_refined0.313
r_nbd_refined0.222
r_symmetry_vdw_refined0.218
r_symmetry_hbond_refined0.183
r_xyhbond_nbd_refined0.166
r_chiral_restr0.096
r_bond_refined_d0.013
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1164
Nucleic Acid Atoms
Solvent Atoms51
Heterogen Atoms13

Software

Software
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing