4AB7

Crystal structure of a tetrameric acetylglutamate kinase from Saccharomyces cerevisiae complexed with its substrate N- acetylglutamate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7277PROTEIN WAS SUBJECTED TO REDUCTIVE METHYLATION OF SURFACE EXPOSED LYSINES WITH ABC PREVIOUS TO CRYSTALLIZATION. 10 MG/ML PROTEIN IN 20MM HEPES PH7.5, 0.5 M NACL, 1MM MSH, AND SUPPLEMENTED WITH 40 MM NAG, WAS CRYSTALLIZED IN PRESENCE OF 0.2 M AMMONIUM CITRATE PH 7.0, 12 % PEG3350 AND 1.5 % PEG 6000 AS CRYSTALLIZATION SOLUTION, IN SITTING DROPS AT 4C. CRYOBUFFER SOLUTION WAS THAT OF CRYSTALLIZATION WITH PEG3350 ENRICHED TO 40%
Crystal Properties
Matthews coefficientSolvent content
2.449

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.883α = 77.31
b = 103.269β = 89.27
c = 111.313γ = 70.43
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2011-05-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

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
13.2510896.20.079.61.9574731.7
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)
13.253.4396.20.461.71.9

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3ZZI3.25108.3654576289696.170.1950.192750.23757RANDOM93.288
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]
0.73-0.51-0.96-0.06-0.46-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.71
r_dihedral_angle_4_deg21.456
r_dihedral_angle_3_deg20.955
r_dihedral_angle_1_deg7.117
r_angle_other_deg1.993
r_angle_refined_deg1.76
r_chiral_restr0.092
r_bond_refined_d0.014
r_bond_other_d0.011
r_gen_planes_refined0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.71
r_dihedral_angle_4_deg21.456
r_dihedral_angle_3_deg20.955
r_dihedral_angle_1_deg7.117
r_angle_other_deg1.993
r_angle_refined_deg1.76
r_chiral_restr0.092
r_bond_refined_d0.014
r_bond_other_d0.011
r_gen_planes_refined0.009
r_gen_planes_other0.009
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_sphericity_bonded
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_symmetry_vdw_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms26294
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing