3ZZF

Crystal structure of the amino acid kinase domain from Saccharomyces cerevisiae acetylglutamate kinase complexed with its substrate N- acetylglutamate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherSTARTING MODEL WAS A LOW RESOLUTION INCOMPLETE MODEL FROM A SE-MET SUBSTITUTED CRYSTAL

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; PREVIOUS TO FREEZING, CRYSTAL WAS SOAKED IN 2 MM HGCL2 AND 25% GLYCEROL AS CRYOPROTECTOR
Crystal Properties
Matthews coefficientSolvent content
2.4349

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.701α = 90
b = 99.299β = 90
c = 190.644γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2009-07-25MSINGLE 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
12.219.971000.12515678651.926.7
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)
12.22.321000.41.915.3

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 REPLACEMENTTHROUGHOUTSTARTING MODEL WAS A LOW RESOLUTION INCOMPLETE MODEL FROM A SE-MET SUBSTITUTED CRYSTAL2.22064245343299.920.18070.17870.21812RANDOM26.165
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]
0.050.06-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.377
r_dihedral_angle_3_deg14.669
r_dihedral_angle_4_deg14.062
r_dihedral_angle_1_deg5.65
r_scangle_it1.966
r_scbond_it1.152
r_angle_refined_deg1.038
r_angle_other_deg0.804
r_mcangle_it0.681
r_mcbond_it0.343
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.377
r_dihedral_angle_3_deg14.669
r_dihedral_angle_4_deg14.062
r_dihedral_angle_1_deg5.65
r_scangle_it1.966
r_scbond_it1.152
r_angle_refined_deg1.038
r_angle_other_deg0.804
r_mcangle_it0.681
r_mcbond_it0.343
r_mcbond_other0.07
r_chiral_restr0.059
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d0.001
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 Atoms8984
Nucleic Acid Atoms
Solvent Atoms430
Heterogen Atoms143

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing