3ZZG

Crystal structure of the amino acid kinase domain from Saccharomyces cerevisiae acetylglutamate kinase without ligands


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.6PROTEIN WAS CRYSTALLIZED IN 50 MM NA-ACETATE, PH 4.6, 0.2 M NA-MALONATE AND 2% PEG 8000,, CONTAINING 24MM N-ACETYLGLUTAMATE (NAG); PREVIOUS TO FREEZING, CRYSTAL WAS WASHED 6 HOURS IN CRYSTALLIZATION BUFFER WITHOUT NAG. 25% GLYCEROL WAS USED AS CRYOPROTECTOR
Crystal Properties
Matthews coefficientSolvent content
2.3848

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.086α = 90
b = 100.531β = 90
c = 188.74γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2011-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
12.952099.80.078.36.4280232.179.7
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)
12.953.1199.80.372.16.5

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 3ZZF2.952026458139899.750.213570.211890.24521RANDOM81.447
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]
2.3-4.041.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.021
r_dihedral_angle_3_deg17.202
r_dihedral_angle_4_deg16.96
r_dihedral_angle_1_deg5.749
r_scangle_it1.585
r_angle_refined_deg1.078
r_scbond_it0.884
r_angle_other_deg0.821
r_mcangle_it0.774
r_mcbond_it0.408
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.021
r_dihedral_angle_3_deg17.202
r_dihedral_angle_4_deg16.96
r_dihedral_angle_1_deg5.749
r_scangle_it1.585
r_angle_refined_deg1.078
r_scbond_it0.884
r_angle_other_deg0.821
r_mcangle_it0.774
r_mcbond_it0.408
r_chiral_restr0.062
r_mcbond_other0.051
r_bond_refined_d0.009
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.001
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_mcangle_other
r_scbond_other
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 Atoms8978
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing