2WXB

Acetylglutamate kinase from Escherichia coli free of substrates


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GS5PDB ENTRY 1GS5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.60.1 M SODIUM CITRATE PH 5.6, 26-32% PEG 4000 AND 0.1-0.3 M AMMONIUM ACETATE
Crystal Properties
Matthews coefficientSolvent content
2.346

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.696α = 90
b = 78.696β = 90
c = 277.743γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH1999-02-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7BEMBL/DESY, HAMBURGBW7B

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
11.952099.80.0511.8635514
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)
122.111000.282.73.6

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 1GS5219.9533717176199.90.2160.2140.247RANDOM42.98
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]
-1.44-0.72-1.442.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.011
r_dihedral_angle_4_deg17.809
r_dihedral_angle_3_deg14.823
r_dihedral_angle_1_deg5.786
r_scangle_it2.33
r_scbond_it1.477
r_angle_refined_deg1.203
r_angle_other_deg0.838
r_mcangle_it0.836
r_mcbond_it0.482
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.011
r_dihedral_angle_4_deg17.809
r_dihedral_angle_3_deg14.823
r_dihedral_angle_1_deg5.786
r_scangle_it2.33
r_scbond_it1.477
r_angle_refined_deg1.203
r_angle_other_deg0.838
r_mcangle_it0.836
r_mcbond_it0.482
r_mcbond_other0.135
r_chiral_restr0.068
r_bond_refined_d0.01
r_gen_planes_refined0.005
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 Atoms3796
Nucleic Acid Atoms
Solvent Atoms176
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing