3ZZH

Crystal structure of the amino acid kinase domain from Saccharomyces cerevisiae acetylglutamate kinase in complex with its feed- back inhibitor L-arginine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ZZFPDB ENTRY 3ZZF

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); 24 HOURS BEFORE FREEZING ARGININE 0.2 M WAS ADDED TO CRYSTALLIZATION DROP. 20% GLYCEROL WAS USED AS CRYOPROTECTOR
Crystal Properties
Matthews coefficientSolvent content
2.4149

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.489α = 90
b = 99.596β = 90
c = 189.238γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2010-09-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM16ESRFBM16

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
12.12099.60.133.84.8770121.919.8
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)
12.12.2199.60.371.94.7

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 3ZZF2.12072907386099.270.182110.180370.21544RANDOM22.225
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]
-0.320.260.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.555
r_dihedral_angle_4_deg17.913
r_dihedral_angle_3_deg13.565
r_dihedral_angle_1_deg5.699
r_scangle_it2.003
r_scbond_it1.143
r_angle_refined_deg1.019
r_angle_other_deg0.801
r_mcangle_it0.649
r_mcbond_it0.326
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.555
r_dihedral_angle_4_deg17.913
r_dihedral_angle_3_deg13.565
r_dihedral_angle_1_deg5.699
r_scangle_it2.003
r_scbond_it1.143
r_angle_refined_deg1.019
r_angle_other_deg0.801
r_mcangle_it0.649
r_mcbond_it0.326
r_mcbond_other0.061
r_chiral_restr0.058
r_bond_refined_d0.007
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 Atoms8953
Nucleic Acid Atoms
Solvent Atoms497
Heterogen Atoms276

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing