4AB7

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ZZIPDB ENTRY 3ZZI

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_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_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_sphericity_bonded
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